VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Mar 04 2014 - 15:39:16 CST

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)
resetpsf
segment PRO {
pdb protein.pdb
mutate 123 whateveryouwantthatisntproline
}
coordpdb protein.pdb
guesscoord
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!
>
> Best,
>
> Joseph
>