Cannot generate protein topology file using Ambertools xleap from data/2020-02-07_tyk2/01_protein/crd/protein.pdb

[victorprincipe]

When processing the file data/2020-02-07_tyk2/01_protein/crd/protein.pdb through xleap (ambertools20) with lig_ejm_44, an error appears when trying to create the topology file of the protein. This appears to be due to a fatal error for 290 atoms where it states that the atom "does not have a type". The following commands were executed in xleap:

source leaprc.protein.ff19SB
source leaprc.water.tip3p
loadAmberParams lig_ejm_44.frcmod
lig = loadMol2 lig_ejm_44.mol2
receptor = loadPDB protein.pdb
complex = combine {receptor lig}
set default PBRadii mbondi3
saveAmberParm lig lig.top lig.crd
saveAmberParm receptor tyk2.top tyk2.crd

--> Error occurs

The same error occurs when the protein.pdb file is processed through pdb4amber prior to generating topologies with xleap. (Note: the lig_ejm_44.frcmod and lig_ejm_44.mol2 files were produced from lig_ejm_44.sdf through antechamber and parmchk2. There was no issue producing topology files for the ligand.)

Please let me know if this is an issue with the .pdb file, or if it's an issue with how it is being processed. Thanks in advance!

Here are the details of the error:

> saveAmberParm receptor tyk2.top tyk2.crd
Checking Unit.

Warning: The unperturbed charge of the unit (-3.000000) is not zero.
FATAL:  Atom .R<ACE 1>.A<HH31 7> does not have a type.
FATAL:  Atom .R<ACE 1>.A<HH32 8> does not have a type.
FATAL:  Atom .R<ACE 1>.A<HH33 9> does not have a type.
FATAL:  Atom .R<PHE 4>.A<HB1 21> does not have a type.
FATAL:  Atom .R<HIE 5>.A<HB1 18> does not have a type.
FATAL:  Atom .R<LYS 6>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 6>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 6>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 6>.A<HE1 26> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HD1 27> does not have a type.
FATAL:  Atom .R<TYR 8>.A<HB1 22> does not have a type.
FATAL:  Atom .R<LEU 9>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 10>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 10>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 10>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 10>.A<HE1 26> does not have a type.
FATAL:  Atom .R<LYS 11>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 11>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 11>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 11>.A<HE1 26> does not have a type.
FATAL:  Atom .R<ILE 12>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 12>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 12>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 12>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 12>.A<HD3 24> does not have a type.
FATAL:  Atom .R<ARG 13>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 13>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 13>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ASP 14>.A<HB1 13> does not have a type.
FATAL:  Atom .R<LEU 15>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLY 16>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLU 17>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 17>.A<HG1 17> does not have a type.
FATAL:  Atom .R<GLY 18>.A<HA1 8> does not have a type.
FATAL:  Atom .R<HIP 19>.A<HB1 19> does not have a type.
FATAL:  Atom .R<PHE 20>.A<HB1 21> does not have a type.
FATAL:  Atom .R<GLY 21>.A<HA1 8> does not have a type.
FATAL:  Atom .R<LYS 22>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 22>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 22>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 22>.A<HE1 26> does not have a type.
FATAL:  Atom .R<SER 24>.A<HB1 12> does not have a type.
FATAL:  Atom .R<LEU 25>.A<HB1 20> does not have a type.
FATAL:  Atom .R<TYR 26>.A<HB1 22> does not have a type.
FATAL:  Atom .R<CYS 27>.A<HB1 12> does not have a type.
FATAL:  Atom .R<TYR 28>.A<HB1 22> does not have a type.
FATAL:  Atom .R<ASP 29>.A<HB1 13> does not have a type.
FATAL:  Atom .R<PRO 30>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 30>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 30>.A<HB1 17> does not have a type.
FATAL:  Atom .R<ASN 32>.A<HB1 15> does not have a type.
FATAL:  Atom .R<ASP 33>.A<HB1 13> does not have a type.
FATAL:  Atom .R<GLY 34>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLY 36>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLU 37>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 37>.A<HG1 17> does not have a type.
FATAL:  Atom .R<MET 38>.A<HB1 18> does not have a type.
FATAL:  Atom .R<MET 38>.A<HG1 19> does not have a type.
FATAL:  Atom .R<LYS 42>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 42>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 42>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 42>.A<HE1 26> does not have a type.
FATAL:  Atom .R<LEU 44>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 45>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 45>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 45>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 45>.A<HE1 26> does not have a type.
FATAL:  Atom .R<ASP 47>.A<HB1 13> does not have a type.
FATAL:  Atom .R<CYS 48>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLY 49>.A<HA1 8> does not have a type.
FATAL:  Atom .R<PRO 50>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 50>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 50>.A<HB1 17> does not have a type.
FATAL:  Atom .R<GLN 51>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 51>.A<HG1 19> does not have a type.
FATAL:  Atom .R<HIE 52>.A<HB1 18> does not have a type.
FATAL:  Atom .R<ARG 53>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 53>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 53>.A<HD1 27> does not have a type.
FATAL:  Atom .R<SER 54>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLY 55>.A<HA1 8> does not have a type.
FATAL:  Atom .R<TRP 56>.A<HB1 25> does not have a type.
FATAL:  Atom .R<LYS 57>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 57>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 57>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 57>.A<HE1 26> does not have a type.
FATAL:  Atom .R<GLN 58>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 58>.A<HG1 19> does not have a type.
FATAL:  Atom .R<GLU 59>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 59>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ILE 60>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 60>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 60>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 60>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 60>.A<HD3 24> does not have a type.
FATAL:  Atom .R<ASP 61>.A<HB1 13> does not have a type.
FATAL:  Atom .R<ILE 62>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 62>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 62>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 62>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 62>.A<HD3 24> does not have a type.
FATAL:  Atom .R<LEU 63>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ARG 64>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 64>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 64>.A<HD1 27> does not have a type.
FATAL:  Atom .R<LEU 66>.A<HB1 20> does not have a type.
FATAL:  Atom .R<TYR 67>.A<HB1 22> does not have a type.
FATAL:  Atom .R<HIE 68>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLU 69>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 69>.A<HG1 17> does not have a type.
FATAL:  Atom .R<HID 70>.A<HB1 18> does not have a type.
FATAL:  Atom .R<ILE 71>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 71>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 71>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 71>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 71>.A<HD3 24> does not have a type.
FATAL:  Atom .R<ILE 72>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 72>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 72>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 72>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 72>.A<HD3 24> does not have a type.
FATAL:  Atom .R<LYS 73>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 73>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 73>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 73>.A<HE1 26> does not have a type.
FATAL:  Atom .R<TYR 74>.A<HB1 22> does not have a type.
FATAL:  Atom .R<LYS 75>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 75>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 75>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 75>.A<HE1 26> does not have a type.
FATAL:  Atom .R<GLY 76>.A<HA1 8> does not have a type.
FATAL:  Atom .R<CYS 77>.A<HB1 12> does not have a type.
FATAL:  Atom .R<CYS 78>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLU 79>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 79>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ASP 80>.A<HB1 13> does not have a type.
FATAL:  Atom .R<GLN 81>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 81>.A<HG1 19> does not have a type.
FATAL:  Atom .R<GLY 82>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLU 83>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 83>.A<HG1 17> does not have a type.
FATAL:  Atom .R<LYS 84>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 84>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 84>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 84>.A<HE1 26> does not have a type.
FATAL:  Atom .R<SER 85>.A<HB1 12> does not have a type.
FATAL:  Atom .R<LEU 86>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLN 87>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 87>.A<HG1 19> does not have a type.
FATAL:  Atom .R<LEU 88>.A<HB1 20> does not have a type.
FATAL:  Atom .R<MET 90>.A<HB1 18> does not have a type.
FATAL:  Atom .R<MET 90>.A<HG1 19> does not have a type.
FATAL:  Atom .R<GLU 91>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 91>.A<HG1 17> does not have a type.
FATAL:  Atom .R<TYR 92>.A<HB1 22> does not have a type.
FATAL:  Atom .R<PRO 94>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 94>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 94>.A<HB1 17> does not have a type.
FATAL:  Atom .R<LEU 95>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLY 96>.A<HA1 8> does not have a type.
FATAL:  Atom .R<SER 97>.A<HB1 12> does not have a type.
FATAL:  Atom .R<LEU 98>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ARG 99>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 99>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 99>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ASP 100>.A<HB1 13> does not have a type.
FATAL:  Atom .R<TYR 101>.A<HB1 22> does not have a type.
FATAL:  Atom .R<LEU 102>.A<HB1 20> does not have a type.
FATAL:  Atom .R<PRO 103>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 103>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 103>.A<HB1 17> does not have a type.
FATAL:  Atom .R<ARG 104>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 104>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 104>.A<HD1 27> does not have a type.
FATAL:  Atom .R<HID 105>.A<HB1 18> does not have a type.
FATAL:  Atom .R<SER 106>.A<HB1 12> does not have a type.
FATAL:  Atom .R<ILE 107>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 107>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 107>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 107>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 107>.A<HD3 24> does not have a type.
FATAL:  Atom .R<GLY 108>.A<HA1 8> does not have a type.
FATAL:  Atom .R<LEU 109>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLN 111>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 111>.A<HG1 19> does not have a type.
FATAL:  Atom .R<LEU 112>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LEU 113>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LEU 114>.A<HB1 20> does not have a type.
FATAL:  Atom .R<PHE 115>.A<HB1 21> does not have a type.
FATAL:  Atom .R<GLN 117>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 117>.A<HG1 19> does not have a type.
FATAL:  Atom .R<GLN 118>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 118>.A<HG1 19> does not have a type.
FATAL:  Atom .R<ILE 119>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 119>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 119>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 119>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 119>.A<HD3 24> does not have a type.
FATAL:  Atom .R<CYS 120>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLU 121>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 121>.A<HG1 17> does not have a type.
FATAL:  Atom .R<GLY 122>.A<HA1 8> does not have a type.
FATAL:  Atom .R<MET 123>.A<HB1 18> does not have a type.
FATAL:  Atom .R<MET 123>.A<HG1 19> does not have a type.
FATAL:  Atom .R<TYR 125>.A<HB1 22> does not have a type.
FATAL:  Atom .R<LEU 126>.A<HB1 20> does not have a type.
FATAL:  Atom .R<HIE 127>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 129>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 129>.A<HG1 19> does not have a type.
FATAL:  Atom .R<HID 130>.A<HB1 18> does not have a type.
FATAL:  Atom .R<TYR 131>.A<HB1 22> does not have a type.
FATAL:  Atom .R<ILE 132>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 132>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 132>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 132>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 132>.A<HD3 24> does not have a type.
FATAL:  Atom .R<HIE 133>.A<HB1 18> does not have a type.
FATAL:  Atom .R<ARG 134>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 134>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 134>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ASP 135>.A<HB1 13> does not have a type.
FATAL:  Atom .R<LEU 136>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ARG 139>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 139>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 139>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ASN 140>.A<HB1 15> does not have a type.
FATAL:  Atom .R<LEU 142>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LEU 143>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ASP 144>.A<HB1 13> does not have a type.
FATAL:  Atom .R<ASN 145>.A<HB1 15> does not have a type.
FATAL:  Atom .R<ASP 146>.A<HB1 13> does not have a type.
FATAL:  Atom .R<ARG 147>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 147>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 147>.A<HD1 27> does not have a type.
FATAL:  Atom .R<LEU 148>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 150>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 150>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 150>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 150>.A<HE1 26> does not have a type.
FATAL:  Atom .R<ILE 151>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 151>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 151>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 151>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 151>.A<HD3 24> does not have a type.
FATAL:  Atom .R<GLY 152>.A<HA1 8> does not have a type.
FATAL:  Atom .R<ASP 153>.A<HB1 13> does not have a type.
FATAL:  Atom .R<PHE 154>.A<HB1 21> does not have a type.
FATAL:  Atom .R<GLY 155>.A<HA1 8> does not have a type.
FATAL:  Atom .R<LEU 156>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 158>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 158>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 158>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 158>.A<HE1 26> does not have a type.
FATAL:  Atom .R<PRO 161>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 161>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 161>.A<HB1 17> does not have a type.
FATAL:  Atom .R<GLU 162>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 162>.A<HG1 17> does not have a type.
FATAL:  Atom .R<GLY 163>.A<HA1 8> does not have a type.
FATAL:  Atom .R<HID 164>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLU 165>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 165>.A<HG1 17> does not have a type.
FATAL:  Atom .R<TYR 166>.A<HB1 22> does not have a type.
FATAL:  Atom .R<TYR 167>.A<HB1 22> does not have a type.
FATAL:  Atom .R<ARG 168>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 168>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 168>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ARG 170>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 170>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 170>.A<HD1 27> does not have a type.
FATAL:  Atom .R<GLU 171>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 171>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ASP 172>.A<HB1 13> does not have a type.
FATAL:  Atom .R<GLY 173>.A<HA1 8> does not have a type.
FATAL:  Atom .R<ASP 174>.A<HB1 13> does not have a type.
FATAL:  Atom .R<SER 175>.A<HB1 12> does not have a type.
FATAL:  Atom .R<PRO 176>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 176>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 176>.A<HB1 17> does not have a type.
FATAL:  Atom .R<PHE 178>.A<HB1 21> does not have a type.
FATAL:  Atom .R<TRP 179>.A<HB1 25> does not have a type.
FATAL:  Atom .R<TYR 180>.A<HB1 22> does not have a type.
FATAL:  Atom .R<PRO 182>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 182>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 182>.A<HB1 17> does not have a type.
FATAL:  Atom .R<GLU 183>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 183>.A<HG1 17> does not have a type.
FATAL:  Atom .R<CYS 184>.A<HB1 12> does not have a type.
FATAL:  Atom .R<LEU 185>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 186>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 186>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 186>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 186>.A<HE1 26> does not have a type.
FATAL:  Atom .R<GLU 187>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 187>.A<HG1 17> does not have a type.
FATAL:  Atom .R<TYR 188>.A<HB1 22> does not have a type.
FATAL:  Atom .R<LYS 189>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 189>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 189>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 189>.A<HE1 26> does not have a type.
FATAL:  Atom .R<PHE 190>.A<HB1 21> does not have a type.
FATAL:  Atom .R<TYR 191>.A<HB1 22> does not have a type.
FATAL:  Atom .R<TYR 192>.A<HB1 22> does not have a type.
FATAL:  Atom .R<SER 194>.A<HB1 12> does not have a type.
FATAL:  Atom .R<ASP 195>.A<HB1 13> does not have a type.
FATAL:  Atom .R<TRP 197>.A<HB1 25> does not have a type.
FATAL:  Atom .R<SER 198>.A<HB1 12> does not have a type.
FATAL:  Atom .R<PHE 199>.A<HB1 21> does not have a type.
FATAL:  Atom .R<GLY 200>.A<HA1 8> does not have a type.
FATAL:  Atom .R<LEU 203>.A<HB1 20> does not have a type.
FATAL:  Atom .R<TYR 204>.A<HB1 22> does not have a type.
FATAL:  Atom .R<GLU 205>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 205>.A<HG1 17> does not have a type.
FATAL:  Atom .R<LEU 206>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LEU 207>.A<HB1 20> does not have a type.
FATAL:  Atom .R<HIE 209>.A<HB1 18> does not have a type.
FATAL:  Atom .R<CYS 210>.A<HB1 12> does not have a type.
FATAL:  Atom .R<ASP 211>.A<HB1 13> does not have a type.
FATAL:  Atom .R<SER 212>.A<HB1 12> does not have a type.
FATAL:  Atom .R<SER 213>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLN 214>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 214>.A<HG1 19> does not have a type.
FATAL:  Atom .R<SER 215>.A<HB1 12> does not have a type.
FATAL:  Atom .R<PRO 216>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 216>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 216>.A<HB1 17> does not have a type.
FATAL:  Atom .R<PRO 217>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 217>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 217>.A<HB1 17> does not have a type.
FATAL:  Atom .R<LYS 219>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 219>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 219>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 219>.A<HE1 26> does not have a type.
FATAL:  Atom .R<PHE 220>.A<HB1 21> does not have a type.
FATAL:  Atom .R<LEU 221>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLU 222>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 222>.A<HG1 17> does not have a type.
FATAL:  Atom .R<LEU 223>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ILE 224>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 224>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 224>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 224>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 224>.A<HD3 24> does not have a type.
FATAL:  Atom .R<GLY 225>.A<HA1 8> does not have a type.
FATAL:  Atom .R<ILE 226>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 226>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 226>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 226>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 226>.A<HD3 24> does not have a type.
FATAL:  Atom .R<GLN 228>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 228>.A<HG1 19> does not have a type.
FATAL:  Atom .R<GLY 229>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLN 230>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 230>.A<HG1 19> does not have a type.
FATAL:  Atom .R<MET 231>.A<HB1 18> does not have a type.
FATAL:  Atom .R<MET 231>.A<HG1 19> does not have a type.
FATAL:  Atom .R<LEU 234>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ARG 235>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 235>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 235>.A<HD1 27> does not have a type.
FATAL:  Atom .R<LEU 236>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLU 238>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 238>.A<HG1 17> does not have a type.
FATAL:  Atom .R<LEU 239>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LEU 240>.A<HB1 20> does not have a type.
FATAL:  Atom .R<GLU 241>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 241>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ARG 242>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 242>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 242>.A<HD1 27> does not have a type.
FATAL:  Atom .R<GLY 243>.A<HA1 8> does not have a type.
FATAL:  Atom .R<GLU 244>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 244>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ARG 245>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 245>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 245>.A<HD1 27> does not have a type.
FATAL:  Atom .R<LEU 246>.A<HB1 20> does not have a type.
FATAL:  Atom .R<PRO 247>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 247>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 247>.A<HB1 17> does not have a type.
FATAL:  Atom .R<ARG 248>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 248>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 248>.A<HD1 27> does not have a type.
FATAL:  Atom .R<PRO 249>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 249>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 249>.A<HB1 17> does not have a type.
FATAL:  Atom .R<ASP 250>.A<HB1 13> does not have a type.
FATAL:  Atom .R<LYS 251>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 251>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 251>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 251>.A<HE1 26> does not have a type.
FATAL:  Atom .R<CYS 252>.A<HB1 12> does not have a type.
FATAL:  Atom .R<PRO 253>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 253>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 253>.A<HB1 17> does not have a type.
FATAL:  Atom .R<CYS 254>.A<HB1 12> does not have a type.
FATAL:  Atom .R<GLU 255>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 255>.A<HG1 17> does not have a type.
FATAL:  Atom .R<TYR 257>.A<HB1 22> does not have a type.
FATAL:  Atom .R<HIE 258>.A<HB1 18> does not have a type.
FATAL:  Atom .R<LEU 259>.A<HB1 20> does not have a type.
FATAL:  Atom .R<MET 260>.A<HB1 18> does not have a type.
FATAL:  Atom .R<MET 260>.A<HG1 19> does not have a type.
FATAL:  Atom .R<LYS 261>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 261>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 261>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 261>.A<HE1 26> does not have a type.
FATAL:  Atom .R<ASN 262>.A<HB1 15> does not have a type.
FATAL:  Atom .R<CYS 263>.A<HB1 12> does not have a type.
FATAL:  Atom .R<TRP 264>.A<HB1 25> does not have a type.
FATAL:  Atom .R<GLU 265>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 265>.A<HG1 17> does not have a type.
FATAL:  Atom .R<GLU 267>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 267>.A<HG1 17> does not have a type.
FATAL:  Atom .R<SER 269>.A<HB1 12> does not have a type.
FATAL:  Atom .R<PHE 270>.A<HB1 21> does not have a type.
FATAL:  Atom .R<ARG 271>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 271>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 271>.A<HD1 27> does not have a type.
FATAL:  Atom .R<PRO 272>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 272>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 272>.A<HB1 17> does not have a type.
FATAL:  Atom .R<PHE 274>.A<HB1 21> does not have a type.
FATAL:  Atom .R<GLU 275>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 275>.A<HG1 17> does not have a type.
FATAL:  Atom .R<ASN 276>.A<HB1 15> does not have a type.
FATAL:  Atom .R<LEU 277>.A<HB1 20> does not have a type.
FATAL:  Atom .R<ILE 278>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 278>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 278>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 278>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 278>.A<HD3 24> does not have a type.
FATAL:  Atom .R<PRO 279>.A<HD1 15> does not have a type.
FATAL:  Atom .R<PRO 279>.A<HG1 16> does not have a type.
FATAL:  Atom .R<PRO 279>.A<HB1 17> does not have a type.
FATAL:  Atom .R<ILE 280>.A<HG11 20> does not have a type.
FATAL:  Atom .R<ILE 280>.A<CD 21> does not have a type.
FATAL:  Atom .R<ILE 280>.A<HD1 22> does not have a type.
FATAL:  Atom .R<ILE 280>.A<HD2 23> does not have a type.
FATAL:  Atom .R<ILE 280>.A<HD3 24> does not have a type.
FATAL:  Atom .R<LEU 281>.A<HB1 20> does not have a type.
FATAL:  Atom .R<LYS 282>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 282>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 282>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 282>.A<HE1 26> does not have a type.
FATAL:  Atom .R<HID 285>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLU 286>.A<HB1 16> does not have a type.
FATAL:  Atom .R<GLU 286>.A<HG1 17> does not have a type.
FATAL:  Atom .R<LYS 287>.A<HB1 23> does not have a type.
FATAL:  Atom .R<LYS 287>.A<HG1 24> does not have a type.
FATAL:  Atom .R<LYS 287>.A<HD1 25> does not have a type.
FATAL:  Atom .R<LYS 287>.A<HE1 26> does not have a type.
FATAL:  Atom .R<TYR 288>.A<HB1 22> does not have a type.
FATAL:  Atom .R<GLN 289>.A<HB1 18> does not have a type.
FATAL:  Atom .R<GLN 289>.A<HG1 19> does not have a type.

Error: Failed to generate parameters
Warning: Parameter file was not saved.
>

@ppxasjsm

[dfhahn]

@victorprincipe To me, it looks like the names of the (mostly) hydrogen atoms are incompatible. Maybe try to

• rename them according to xleap-compatible names?
• remove the hydrogen atoms from the pdb beforehand.

Thanks for raising this issue. Would be great if the pdb files were compatible with Amber.