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:
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 Thu Sep 22 2005 - 16:53:01 PDT