Re: Custum made residue addition

From: Chitrak Gupta (
Date: Fri Apr 28 2017 - 08:11:31 CDT

Hi Zeki,

Remember to do "reply all" so that others can chime in as well as the
conversation goes to the archive.

If you do have the topology/parameter files then life becomes a lot easier.
I don't know how to do it using the mutator plugin, but if you use the
script given in the NAMD tutorial (the "setup.pgn" script, in the
"Generating a Protein Structure File (PSF)" section), you can modify it
slightly. Read in the topology file of your residue along with the standard
protein topology file, and then when reading in the PDB file, do this:

segment U {
pdb yourPDBfile.pdb
mutate n XXX

where n is the position where you want to mutate and XXX is the residue
code as defined in the topology/parameter file.

Then proceed as normal. That should do it.

Hope this helps,

On Fri, Apr 28, 2017 at 2:52 AM, Zeki Zeybek <>

> I do have the parameter file but I do not know how I can add the new
> residue into pdb so that I can construct psf file and proceed. Because atom
> numbers are shifted when I add the new residue
> ------------------------------
> *From:* Chitrak Gupta <>
> *Sent:* 27 April 2017 22:46:27
> *To:* NAMD list; Zeki Zeybek
> *Subject:* Re: namd-l: Custum made residue addition
> Hi Zeki,
> Do you have a parameter file for this custom residue? If not, you probably
> need to look into something like the FFTK plugin in VMD to parameterize the
> residue.
> Chitrak.
> On Thu, Apr 27, 2017 at 9:08 AM, Zeki Zeybek <>
> wrote:
>> Hi!
>> I would like to mutate a few Lysine residues into a custom made residue.
>> I have looked for some options such as Mutator plugin, pdb file mutation
>> etc. Mutator helps only when you need to mutate the residue into known
>> aminoacids and pdb file manipulation is a long process. Hence I would much
>> appreciate if anyone can help me with this. Thank you all.

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:14 CST