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:
Ø 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
