AMBER Archive (2005)

Subject: AMBER: How to split LES trajectory using TRAJ

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Thu Sep 22 2005 - 10:12:51 CDT


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

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  ----- Original Message ----- 
  From: Melinda Layten 
  To: amber_at_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_at_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:

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

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----- Original Message ----- From: "Carlos Simmerling" < carlos.simmerling_at_stonybrook.edu> To: <amber_at_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 >> > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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