Parametrization problems

[DanieleDiMarino]

Hi, I'm trying to convert from atomistic to coarse grained a small molecule but I got errors and I don't know how to solve them. I have installed ato-martini with the right dependencies My first question is: Is possible that my molecule is too big? This is the command line:

./auto_martini --smi "o1c(nc(n1)c1ccccc1)[C@H]1NH" --mol CP6 --gro CP6.gro --verbose

This is what I got:

; ring atoms: [[0, 1, 2, 3, 4], [5, 6, 7, 8, 9, 10], [19, 20, 21, 22, 27, 28]] ; Heavy atoms: O C N C N C C C C C C C N C C N C O N C C C C C F F F C C C Error. Exhaustive enumeration can't handle large molecules. Number of heavy atoms: 30 python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed. Annullato (core dump creato)

Now

(I have converted the pdb structure in smile format using babel) P.s. If my molecule is really too large can I use the auto-martini to convert my molecule in CG dividing it in small sub functional groups and than putting everything together?

Thank very very much Daniele

[tbereau]

Hi Daniele,

Yes, the code currently only supports up to 25 heavy atoms. An updated version is in the works, but it's not quite ready yet. In the meantime, I would indeed recommend you to cut the molecule into pieces (2 should work in this case), and later stitch them together by editing the topology files.

Good luck!

Best, Tristan

[Kuchenbecker]

Dear @tbereau, one question: I understand how to actually break a molecule into two pieces, generate the .itp files and put them together. But how to create a single .gro file after diving the molecule? I mean, how to match the coordinates. Thanks.

[tbereau]

Unfortunately there's no automated way to do that--not that I know of. You can try to rototranslate the molecules so that they're relatively well aligned, and then do some gentle energy minimization and equilibration. Might do the trick.