AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 05 2007 - 11:04:12 CDT

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

no, you use the original prmtop to read the old mdcrd and strip water

trajin mdcrd
strip :WAT
trajout nowat.mdcrd

for the energy analysis, there is an example in test/trajene that you can
follow.
use the no-water prmtop with the no-water mdcrd file.

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
> >
> >
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>
>
>
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