Re: AMBER: How to split LES trajectory using TRAJ

From: Melinda Layten <mlayten.gmail.com>
Date: Wed, 21 Sep 2005 16:09:29 -0400

It's at the very bottom of the page. I'm just forwarding the link:

 Carlos's undocumented AMBER analysis program V2.0 (July
2003)<http://morita.chem.sunysb.edu/%7Ecarlos/viewpage/analysis.tar.gz>



On 9/19/05, Xin Hu <hux.mail.rockefeller.edu> wrote:
>
> Dear Dr. Simmerling,
> I have checked the Amber Archive about the the LES-MD analysis, and
> someone
> postered that it is possible to use "ptraj " to split the LES trajectory
> (Sorry, not "traj"). (see below). I wonder how it works?
>
> Also I read a response from you about the energy analysis of LES-MD, you
> suggested "the only option is to split the trajectory into separate single
> copy trajectories and run mm-pbsa type analysis. here's my suggestion:
> download my "analysis" program from the moil-view page, and split the
> trajectory. then use the imin=5 option in sander (amber7) to evaluate the
> energies of each copy.". However, I did not find such a "analysis" program
> on your website.
>
> I tried the MOIL-VIEW program using the command "pick" and #cop to
> separate
> the LES-MD to a single copy, but seems it is not working. The LES region
> in
> my protein (214 aa) is a loop consisting of 10 aa, I divided it into three
> segments (92-94, 95-98, 99-101) and each was assigned five copies. After
> LES
> simulation, should I use the following command to get each sigle copy
> trajectory?
>
> pick #mon 1 91 |#mon 91 101 &cop 1 |#mon 102 214 done
> pick #mon 1 91 |#mon 91 101 &cop 2 |#mon 102 214 done
> pick #mon 1 91 |#mon 91 101 &cop 3 |#mon 102 214 done
> .......................
>
> Thank you very much for your help.
>
>
> Xin
>
> PS:
>
>
> 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?
> 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
>
> ---
>
>
>
>
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.stonybrook.edu>
> To: <amber.scripps.edu>
> Sent: Monday, September 19, 2005 1:40 PM
> Subject: Re: AMBER: How to split LES trajectory using TRAJ
>
>
> > what is "TRAJ"?
> >
> > Xin Hu wrote:
> >
> >> Dear Amber user,
> >> Does anyone give me some suggestions on the analysis of LES result
> using
> >> TRAJ (to seperate the trajectory)? I apprecite very much if you could
> >> show me a simple script.
> >>
> >> Thanks in advance.
> >>
> >>
> >> Xin
> >>
> >
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>
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Received on Wed Sep 21 2005 - 21:53:00 PDT
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