AMBER Archive (2004)

Subject: Re: AMBER: ptraj & LES

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Feb 02 2004 - 11:22:09 CST

Thanks,
   its funny ...i didnt even think of that although its probably the
easiest way...I have only 5 copies so it should not be so difficult....
Vlad

Michael Trieb wrote:

> Dear Vlad,
>
> I am quite sure that it is also possible with ptraj, but for me CARNAL
> worked (and I think in both cases you have to specify the atoms
> belonging to each copy...and that's the time consuming part).
> In my case I had DNA and a ligand, and part of the ligand I defined as
> my LES region
> Here a sample file:
>
> FILES_IN
> PARM p1 prmtop;
> STREAM s1 *.mdcrd;
> FILES_OUT
> COORD c1 name1.crd CRD;
> COORD c2 name2.crd CRD;
> COORD c3 name3.crd CRD; ...
> DECLARE
> GROUP g1 (ATOM 1-890, 1091-1118, 1319-1338); #DNA
> GROUP g2 (ATOM
> 891,896,901,906,911,916,921,926,931,936,941,....); #every 5th
> atom of LES region 1st copy
> GROUP g3 (ATOM.......); #every 5th atom of LES region 2nd copy...
> GROUP g12 ((GROUP g1) | (GROUP g2)); #DNA+1st copy
> GROUP g13 ((GROUP g1) | (GROUP g3)); # DNA+2nd copy
> OUTPUT
> COORD c1 GROUP g12;
> COORD c2 GROUP g13;........
> END
>
> Hopefully you don't have too many copies....
>
> Michael
>
> Vlad Cojocaru wrote:
>
>> Dear Amber users,
>> I read a message (a while ago) that ptraj can separate the LES
>> trajectory into separate trajs for each copy. Has anyone ever done that?
>> Best wishes
>> vlad
>>
> 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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