RE: About "mutate" command in psfgen package.

From: JC Gumbart (
Date: Thu Feb 02 2006 - 23:06:44 CST

segment U {pdb aaa.pdb
mutate resid 4 GLN}


I believe the new line after the pdb is very important here.



From: Boyang Wang []
Sent: Thursday, February 02, 2006 10:56 PM
To: JC Gumbart;
Subject: Re: namd-l: About "mutate" command in psfgen package.


Thanks for your reply.


I tried several options, including


"segment U {pdb aaa.pdb mutate resid 4 GLN}"


"segment U {pdb aaa.pdb}
mutate resid 4 GLN"


Followed by


"coordpdb aaa1.pdb U

writepdb ala1.pdb
writepsf ala1.psf

And at the beginning, I put


"package require psfgen
topology top_all22_prot.inp"

Vmd Tkconsol always gives this information:


"building segment U
reading residues from pdb file aaa1.pdb
extracted 3 residues from pdb file
Info: generating structure...
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
too many arguments specified
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over."


If you are interested, you can have a try.


Thanks again.



JC Gumbart <> 写道:

I think the mutate command goes in your segment generation statement.

So instead of

> mutate resid 4 GLN
> segment U {pdb aaa.pdb}


segment U {pdb aaa.pdb
mutate resid 4 GLN}

On Feb 2, 2006, at 5:24 PM, Boyang Wang wrote:

> Hi all.
> I am trying to use "mutate" command in the psfgen package.
> If I have a peptide AAA, and I want to mutate the third residue (resid
> 3) "A" to glycine, it shows that "mutate 3 GLY" is not the right
> command to use in the *.pgn file.
> The tutorial shows that
> " mutate "
> ----- : Unique name for residue, 1–5 characters, usually
> numeric.
> So what is wrong then?
> The pdb file is a peptide AAA, the pgn file is as follows:
> "
> package require psfgen
> topology top_all22_prot.inp
> mutate resid 4 GLN
> segment U {pdb aaa.pdb}
> coordpdb aaa.pdb U
> guesscoor
> writepdb aag.pdb
> writepsf aag.psf
> exit
> "
> Thanks for all your time.
> Boyang.

Boyang Wang,
Email -
Major - Phys. Chem.
dept Chemistry,
Univ Illinois, Chicago,
60607 IL US.


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