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

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 18 08:31:16 CEST 2018


The name of the residue in that force fields aminoacids.rtp is CLA, which
is the only thing pdb2gmx can understand. Otherwise your procedure should
just work if you rename your ion residues appropriately. Do let us know how
you go!


On Wed, Jul 18, 2018, 03:23 Anderson, Amos <Amos.Anderson at pfizer.com> wrote:

> 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,
> Amos.
> 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.
> --
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