Re: AMBER: How to split LES trajectory using TRAJ

From: Xin Hu <hux.mail.rockefeller.edu>
Date: Mon, 19 Sep 2005 16:49:47 -0400

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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Received on Mon Sep 19 2005 - 21:53:00 PDT
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