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
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Received on Fri Apr 15 2011 - 06:00:03 PDT
