Respected Sir,
Thank you very much for your suggestion. I will definitely rerun the
simulation.
Just a silly query, what could be the role of atomic number in MD
simulation?
Looking forward for your reply
Regards
On Tuesday, December 27, 2016, David A Case <david.case.rutgers.edu> wrote:
> On Mon, Dec 26, 2016, A kS wrote:
> >
> > In order to simulate a modified residue I have used a perpin and frcmod
> > file corresponding to the modification.
> >
> > In that prepin and frcmod file I used an new atomtype for an atom
> Sulphur.
> > Like a standard prepin and frcmod file, information regarding this
> atomtype
> > are given in those files except the hybridization state,
> >
> > I forgot to add this atomtype in tleap file by using command
> "AddAtomtype".
> > As a result leap gives a warning "Unknown atomtype".
> > I am not sure whether this cause any major problem or not, because I
> think
> > necessary parameters for this atomtype, except hybridization state, are
> > given in the respective prepin and frcmod files.
>
> Probably safest to re-run things with the AddAtomType command. The
> hybridization means very little, but this command also establishes the
> element (atomic number). If you atom type begins with "S" or "s", you are
> probably OK, but you should probably check the atomic number in the prmtop
> file just to be sure.
>
> ...dac
>
>
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Received on Mon Jan 02 2017 - 09:00:02 PST
