[gmx-users] Regarding finding a ion/molecule in forecefield

Justin Lemkul jalemkul at vt.edu
Fri Dec 29 14:29:07 CET 2017

On 12/29/17 8:25 AM, Dilip H N wrote:
> 1] I wanted carbonate ion with -2 ion charge. (i checked in atomtypes.atp
> where, carbonate  is mentioned as "CG2O6 12.01100 ; carbonyl C: urea,
> carbonate",  "OG2D2  15.99940 ; carbonyl O: negative groups: carboxylates,
> carbonate").

Nothing in the .atp file is useful here. What I told you is what you 
wanted, the CO3 residue (in the merged.rtp file) has a -2 charge.

> And i also checked with ions.itp (in which the ions are represented), but i
> could find only calcium with +2 charge and not carbonate ion. (hope while
> converting from gmx pdb2gmx is it converted into an ion ..??)

pdb2gmx never reads ions.itp - it reads .rtp files. You'll find both 
species there.

> 2] In general how can i find/search for the required molecule and in which
> forcefield is it present in...?

You have to go to the source force field files. GROMACS files don't give 
you any information about what residues are; they assume you know. If 
you download the CHARMM36 tarball from the MacKerell website and in the 
toppar directory, issue:

grep -ri "carbonate" * | grep RESI

you will find what you need. Then just check that the same residues are 
defined in the GROMACS .rtp file and proceed.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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