make the no-water prmtop the same way that you made your original prmtop.
I can't help with that since you did it yourself.
On 7/5/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> no-water.prmtop file is not created in this command.then how can one do
> that
> for energy analysis i can use the test/trajene.
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
>
>
> On 7/5/07, priya priya <priyaanand_27.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.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.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.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.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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Received on Sun Jul 08 2007 - 06:07:26 PDT
