Dear Gustavo,
I choose atom number from the PDB file that create by leap.
When I made file preparation file using tleap usually I also save box file
using SavePDB.
Am I correct to choose atom numbers from PDB file that I got from tleap ?
regards
setyanto
On Fri, Apr 15, 2011 at 7:45 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> On Friday, April 15, 2011, Jason Swails <jason.swails.gmail.com> wrote:
> > 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,"
>
> Just to add to Jason's answer, note that the atom numbers that go here
> are *not* the atom numbers of the PDB file, but the sequential atom
> number from the amber input (prmtop, inpcrd), which is not necessarily
> the same as in the PDB file. You can get the correct atom numbers by
> opening the amber input in a program such as VMD and checking the
> numbering.
>
> Gustavo.
>
> --
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 17 2011 - 21:00:02 PDT
