Re: phosphoserine simulation using toppar files and NAMD

From: L. Michel Espinoza-Fonseca (
Date: Wed Mar 25 2009 - 07:55:45 CDT

Hi Henrik,

In order to avoid this problem, you need to regenerate the angles and
torsions of the added patch. You can do that by adding the 'regenerate
angles dihedrals' line to your input file. Alternatively, you can
select this option in the autopsf generation tool of VMD (in case you
used it).


On Wed, Mar 25, 2009 at 12:55 PM, hgrabner <> wrote:
> 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.
> Additionally:
> 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!
> Henrik

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