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: Fri Jul 06 2007 - 07:25:02 CDT

priya priya <priyaanand_27_at_yahoo.co.in> wrote: Dear Sir,

I am running my simulations in explicit solvent, if i want the energy of peptide , i can strip water molecules for it. But that will not include the interactions of the water molecules with it. so after excluding the water molecules from the trajectory and in calculating the energy can i add the implicit solvent by using igb=1.
Regards

Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

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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