From: Daou, Joseph A (
Date: Tue Mar 04 2014 - 19:53:37 CST

Thank you for the help, Josh!

Here is another question.

I tried to turn the Free energy perturbation calculation with the mutation of Pro--> X (X=any amino acid). In my case X is H (Histidine). NAMD2 could not recorgnize P2H topology. Do you have a hybrid topology for Pro--> H mutation to run Free energy perturbation? If not, can I generate such a topology file by myself?


From: Josh Vermaas <>
Sent: Tuesday, March 04, 2014 4:39 PM
To: Daou, Joseph A;
Subject: Re: vmd-l: Mutate Residue Extension

Hi Joseph,

Have you tried running mutator from the tkconsole? If so, what is the error message exactly? Mutating from a proline to anything else is procedurally no different than mutating any other residue. What might cause a problem in VMD 1.9.1 is if the resid for the residue has an insertion code in it (48A instead of just 48), which would make psfgen in that version very very unhappy. With the exact error message, it would be easier to pin down exactly what is going on.

FYI, the mutate residue plugin is just a frontend for psfgen, so what it does is basically the following:

#psfgen setup
package require psfgen
topology charmblahblahblah.rtf
#Now build the psf/pdb pair (I'm assuming your protein has one segment, with the mutation occuring at resid 123)
segment PRO {
pdb protein.pdb
mutate 123 whateveryouwantthatisntproline
coordpdb protein.pdb
regenerate angles dihedrals
writepsf new.psf
writepdb new.pdb

So if it comes down to it, you could play around with a script like that to build it however you want.
-Josh Vermaas

On 03/04/2014 02:25 PM, Daou, Joseph A wrote:

Dear VMD specialists,

I am an undergraduate Biochemistry researcher at the University of New Haven. I had a question regarding the "Mutate Residue" extension. I am having trouble mutating the Proline residues on my protein to another amino acid. The mutator cannot recognize where proline is on a specific protein we are studying. Do you have any suggestions on other methods to try? I would even greatly appreciate any advice on this issue.

Thank you in advance for the help!