[gmx-users] pdb2gmx: how to preserve original ions?

Anderson, Amos Amos.Anderson at pfizer.com
Wed Jul 18 03:22:44 CEST 2018

Hi Gromacs users,

I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for…

I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The input pdb to my script may have waters, ions, and ligand(s) in it already. In the tutorial it says "you are going to want to strip out the crystal waters, PO4, and BME. Note that such a procedure is not universally appropriate (i.e., the case of a bound active site water molecule).” The wording maybe implies that other than active site waters and the ligand of interest, I’d never want to preserve HETATOMs in my input file?

If not, and if I do want to keep them, how do I? Do I just treat all of them like ligands in the tutorial, e.g., maybe a protocol like this (more precise for ions I care about)?

     *   grep HETATOM my.pdb > hetatoms.pdb
     *   gmx editconf -f hetatoms.pdb -o hetatoms.gro
     *   copy/paste hetatoms.gro into my main .gro file (is there python/utility anywhere for merging .gro files I could leverage?)
     *   for ions gromacs doesn’t already know about (ions.itp), follow the instructions described here: http://www.mdtutorials.com/gmx/complex/02_topology.html

(in other words, I’m puzzled why pdb2gmx is complaining about ions it should already know about from the built-in ions.itp)

Thanks for any advice,

To help future googlers, I run pdb2gmx on a file that has CL in it like this:

gmx_d pdb2gmx -v -o output.gro -p output.top -ignh -water tip3p -ff charmm27 -f my.pdb

 I get this error:

Program:     gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'CL' 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

which surprises me because CL is defined in ions.itp. It says it’s finding other files in the same directory as ions.itp, so it doesn’t seem like some kind of misconfigured software install.

More information about the gromacs.org_gmx-users mailing list