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