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

Marko Sever Marko.Sever at ki.si
Fri Mar 24 11:25:09 CET 2017

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?
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?

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: /share/apps/gromacs/5.1.2/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 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...

Thanks for the help!

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