phosphoserine simulation using toppar files and NAMD

From: hgrabner (
Date: Wed Mar 25 2009 - 06:55:56 CDT

Hello everybody!

I have the following problem:
In my simulation, the oxygen atoms of a phosphorylated serine are
reorientating themselves in a way that they are occupying the same
space (looks like there is only one terminal oxygen instead of three).

How I started the simulation:
I used psfgen in VMD to create a psf file using the topology files:
top_all27_prot_na.rtf & toppar_prot_na_all.str. I applied the SP2
patch. The resulting structure looks fine to me...
For a fast check, I started a minimization run using the namd
interface in VMD (version 1.8.6). I used the parameter file
par_all27_prot_na.prm and again the toppar_prot_na_all.str file.

I read in this mailing list, that you have to copy/paste the relevant
phosphoserine information from the stream file
"toppar_prot_na_all.str" into the top_all27_prot_na.rtf and
par_all27_prot_na.prm file. I did this, too and restarted the whole
simulation. The result was again a reorientation of the oxygen atoms
like described above.

I got the toppar files from this website:

Thanks for any help and comments!


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