[gmx-users] Regarding finding a ion/molecule in forecefield
Dilip H N
cy16f01.dilip at nitk.edu.in
Fri Dec 29 14:25:44 CET 2017
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,
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 ..??)
2] In general how can i find/search for the required molecule and in which
forcefield is it present in...?
On Fri, Dec 29, 2017 at 6:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/29/17 7:43 AM, Dilip H N wrote:
>> Hello all,
>> How to find out/search a specific molecule or ion is present in which
>> forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
>> molecule), and hence can generate .pdb file corresponding to that residue
>> naming in the FF and generate its topology.
>> In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
>> which forcefield is it present.
>> Any suggestions...
> Both are in CHARMM36. Ca2+ is CAL and carbonate is CO3.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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