AMBER Archive (2007)

Subject: Re: AMBER: How to extract energy of molecule from the system with explicit water molecules

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Thu Jul 05 2007 - 10:57:59 CDT


I am not able to understand what exactly you are saying.
lets me say in my words,
>From the Md run i have final mdcrd and rst files, using them i create a pdb file using ambpdb command and then make prmtop file using leap. Using this prmtop file i will remove water molcules using the ptraj >strip (water): command.
then how can i write a new mdcrd file from this and how to use sander command.
Sorry if i am asking the very basic step.
Regards

Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote: the easiest way is to do what I suggested, make a new prmtop in
leap and then use ptraj to strip the water and write a new mdcrd file.
then you can use sander to read in this trajectory with the imin=5
option and it will write energy for each frame. check page 90 of the
amber9 manual but note that the input trajectory is specified with -x,
not -y.

On 7/5/07, priya priya < priyaanand_27_at_yahoo.co.in> wrote:Hi,
i want to extract the potential energy of the peptide without including the water molecules and not including the interaction of peptide with water.
I want it to calculate all the frames of the trajectory,
Regards
priya

Carlos Simmerling < carlos.simmerling_at_gmail.com> wrote: do you mean just the internal energy, or also the interaction with
water? the latter is difficult in a periodic system. if you want just
the peptide energy, you can use ptraj to strip the water and then
make a prmtop of just the peptide without water. then you can
evaluate the energy of the peptide. if you want more specific suggestions
you'll need to make clear what you want- energy for a restart
file, or for all frames in the trajectory, energy with or without peptide:water
interaction, and so on.

On 7/5/07, priya priya < priyaanand_27_at_yahoo.co.in> wrote: Dear All

I am interested in extracting the energy of the molecule i.e peptide only from the output file that i obtained from running MD of that peptode in explicit solvent (water).

Please suggest me something!
Regards
 

         

---------------------------------
  Here's a new way to find what you're looking for - Yahoo! Answers

 

 Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu