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From: Hurt, Darrell (NIH/NIAID) [E] (darrellh_at_niaid.nih.gov)
Date: Tue Dec 21 2010 - 11:18:00 CST

I think the mutation tool in the VMD GUI will work for you and build the PSF automatically.

Extensions > Modeling > Mutate Residue

On 12/20/10 10:29 PM, "Bharat Kumar" <bharat.stanam_at_gmail.com> wrote:

Hi,

I want to replace a wildtype protein in an embedded POPC membrane with a mutant one. I loaded the wild-type, embedded in membrane, and the mutant PDBs. I used the RMSD calculator to calculate RMSD and then aligned the backbone CA atoms of mutatnt with that of wildtype. Now I want to 1) save the coordinates of the mutant and the membrane without wildtype as a single PDB file and 2) To generate PSF for this PDB file.

Can you please give me some directions in achieving first the first job and then the second task?

sincerely,
Bharat.

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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