AMBER: How to split LES trajectory using TRAJ

From: Xin Hu <hux.mail.rockefeller.edu>
Date: Thu, 22 Sep 2005 11:12:51 -0400

Hi Melinda,
Thank you very much for your help. I tested Dr. Simmerling's program "analysis" using the LES example in Amber8. For the "enter topology filename", while I gave the input "LES.top", it showed an error: "

AMBER 4.1 style LES not detected
Error reading initial variable list in parm file
problem reading paramenter file

It seems the program is for the old version Amber4.1. Could you give me some suggestions?

Thank you very much.



Xin

---
  ----- Original Message ----- 
  From: Melinda Layten 
  To: amber.scripps.edu 
  Sent: Wednesday, September 21, 2005 4:09 PM
  Subject: Re: AMBER: How to split LES trajectory using TRAJ
  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)
  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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Received on Thu Sep 22 2005 - 16:53:01 PDT
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