My another concern is to change the cut-off parameter from 100(default) to
12 A while minimization using minab.
I copied minab.c and minab.nab file into my local directory and changed the
values, but could not succeed.
Somewhere I read about recompilation...dont know how to do it. Also, I want
to know about MPI implementation in NAB .
Many Thanks
On Mon, Dec 9, 2013 at 10:41 AM, sunita gupta <sunita.bio.gmail.com> wrote:
> Thanks a ton.
>
>
> On Sun, Dec 8, 2013 at 9:59 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Sun, Dec 08, 2013, sunita gupta wrote:
>>
>> > I have a protein-lignad complex (231 residues protein and 232nd residue
>> as
>> > ligand). While setting up MD for this complex I want to fix the protein,
>> > and if I am selecting ':1-231' as restrainmask, it is selecting the
>> ligand
>> > as well.
>>
>> NAB atom expressions are different than those in the rest of Amber: they
>> have three sections (chain (aka strand, aka molecule), residue, atom), and
>> the residue numbers start over at 1 for each new chain.
>>
>> Hence, you atom expression selects residues numbered 1-231 in each chain:
>> this
>> will include the ligand (which is presumably the first residue in the
>> second
>> chain.) What you probably want is "1::" (for the entire first molecule).
>>
>> ...good luck...dac
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> --
> SUNITA GUPTA
> Senior Research Fellow
> Bioinformatics Centre
> Jawaharlal Nehru University
> New Delhi- 110067
> Email- sunita.bio.gmail.com
>
>
>
>
--
--
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 08 2013 - 21:30:03 PST
