Hello,
On Thu, Apr 14, 2011 at 9:25 PM, setyanto md <stwahyudi.md.gmail.com> wrote:
> Dear amber user and developer
>
> I am doin qmmm simulation. I'd like to mask atom rather than residue. Here
> is list of atoms from my pdb file:
> :
> ATOM 935 CG ASP 61 -4.452 12.837 -8.642 1.00 0.00
> ATOM 936 OD1 ASP 61 -5.589 12.636 -8.154 1.00 0.00
> ATOM 937 OD2 ASP 61 -3.962 13.964 -8.866 1.00 0.00
>
> I've been read in page 91 manual of Amber 10. we can use iqmatoms to mask
> our QM region.
>
> So I do like this :
>
> iqmatoms='.935,936,937',
>
No. This is an integer list. Just put "iqmatoms=935,936,937,"
>
> My question is :
> 1. Is this correct or not ?
> 2. How to calculate qmcharge according my QM definiiton? as I know that
> charge of C is 0, O is -2, so total charge is -4, right or wrong ?
>
You have to determine how many electrons will be present total. Carboxylate
groups typically only have a 1- charge. In case this is not just an
example, performing QM/MM simulations *just* on a carboxylate group of a
given residue doesn't seem like a realistic simulation to me. Consult the
literature (there is a lot of it) on QM/MM calculations to look into common
protocols.
Hope this helps,
Jason
> Thank you verymuch for your help.
>
> regards
>
> setyanto tri wahyudi
> ITB-Biokimia
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 14 2011 - 22:00:03 PDT
