conversion of Amber files to gromacs

Open Pz-Maajid opened this issue 2 years ago • 3 comments

I am converting the two files that is UNL.parm7 and UNL.rst7 , which I got from ambertools, to gromacs using acpype. But the gro file which I got from this conversion has some bond missing in it when I am opening it in VMD .I want to know the reason ,why this is happening . .

Jun 08 '23 18:06 Pz-Maajid

A .gro file does not contain bond information. Thus, VMD infers and draws the presence or absence of a bond by the distance of the atoms. The distance between pairs of atoms may be longer than the cut-off. Could you check the distance of these missing bonds?

Jun 12 '23 05:06 riquri

It is 1.93 and 1.8 A for the missing bonds .Can you please tell how to solve the issue .

Jun 12 '23 06:06 Pz-Maajid

How? I don't have the input files.

Jun 12 '23 07:06 alanwilter