Hi Paer,
Thank you very much for your mail.
Here is the paper from where we are taking the MTSSL parameters
J. Phys. Chem. B 2008 112, 5755-5767, by B. Roux
and the supplementary in it.
Thank you.
Sudip
Pär Bjelkmar wrote:
Hi,
21 okt 2009 kl. 10.59 skrev Sudip Roy:
Thank you very much for your reply.
MTSSL is not a peptide, but it was parameterized by some
other group and we are trying to use the parameters. They have
used CMAP for MTSSL. So we also want to
take into account the CMAP in our gromacs calculations.
This is very strange! You are sure the molecule works in CHARMM? I
mean there's only three CMAPs parameterized in the CHARMM force field;
ALA, PRO and GLY and MTSSL does not contain any amino acids so I guess
must have parameterized new CMAPs then. I would very much like to see
the CHARMM definition of this molecule if you don't mind.
I am not much familiar with git repo. It will be very kind of you
if you send us a copy of gromacs 4.1 and CHARMM27 ff file
with CMAP in gromacs format, so that we can include this
ff also in our database.
Well, follow the instructions here:
http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage
and compile the source (instructions on the webpage also) on your
platform.
Then place the ffcharmm27 files in the attachment in the current
working directory (or place them in the share/top/ directory of the
installation).
Regards,
Pär Bjelkmar
--
**********************************************************************************************
Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India
Tel. +91 2590 2735 Office
Email s....@ncl.res.in
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