Re: vmd-l: Proper use of psfgen "mutate"?

From: Francesco Pietra (
Date: Tue Apr 10 2018 - 09:20:20 CDT

I always found that such affairs are managed correctly by CHIMERA, a
software that I use for what is much simpler than with VMD (movie
representing the pathway of a ligand under MD), or for what VMD does not
understand (pdbqt files from docking)


On Tue, Apr 10, 2018 at 3:58 PM, Brian Radak <> wrote:

> The user guide is unfortunately lacking in good examples for this.
> I have a simple, complete peptide structure for (ALA)_5 and want to make a
> new PSF/PDB with psfgen after converting the central residue (resid 3) to
> ASP. The mutate command sounds perfect for this. I did something like the
> following:
> segment PROA {
> pdb foo.pdb
> mutate 3 ASP
> }
> coordpdb foo.pdb PROA
> guesscoord
> which works, but predictably has trouble reading the PDB since it finds
> the atom HB3 in ALA when it is expecting CG, etc. from ASP. The guessed
> coordinates for the added carboxylate are fairly atrocious with a
> completely unphysical dihedral. Is this an expected limitation of mutate?
> Obviously it is a bit too much to ask that mutate immediately figure out
> the mapping between those two atoms on-the-fly. I was able to tell psfgen
> about that mapping by adding:
> pdbalias atom ALA HB3 CG
> before reading coordinates, but I'm pretty sure this is a global mapping
> that discards the HB3 coordinates for all other ALA residues (not what I
> want). This works out just fine in my case, but seems unsatisfying as the
> solution to the problem in general. Is there a more specific workaround
> than this? What would I do for a more complicated mutation like LYS to TYR?
> Cheers,
> Brian

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