[gmx-users] Getting charges of the system out of the simulation in human-readable form

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 24 12:03:23 CET 2017


On Fri, 24 Mar 2017 11:25 Marko Sever <Marko.Sever at ki.si> wrote:

So my question is, what is the most simple way to get a file with residue
and atom types in addition to charges out of the files created at the end
of the simulation?

There isn't one apart from what is written by eg gmx editconf -s your.tpr
-o a.pdb or similar. That is a very verbose and redundant representation.
The tree-like structure of the .top and .tpr file is more useful for
everything except "what is the type of atom 2948" etc.

The return question is "Why is it more suitable to have the tree fully
written out on order to make such queries?"

I tried dumping the .tpr file but its file structure is a bit too
complicated, I'd preffer something easier. Also since I created the input
files with Charmm-gui I got a lot of .itp files, but I would preffer to
have just one?

The separate files make re-use in different simulations easier to manage.
Why is one file more useful?

Also if I make again a new pdb of the system and go with gmx pdb2gmx ->
"gmx pdb2gmx -f mdforpsf.pdb -o prcs.gro -ff charmm36chol_psm_dopc -water
tip3p" it errors out with the following error:

Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
line: 645

Fatal error:
Residue 'PSM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

While PSM.itp is located in the charmm36chol_psm_dopc.ff folder, and other
many itp files get read fine...weird...

Charmm gui and pdb2gmx do the same job as each other: producing itp files.
Pdb2gmx is complaining about missing rtp files, which nothing has provided.


Thanks for the help!
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