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

[Justin Lemkul]

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

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

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