[gmx-users] Re: CMAP request

Sudip Roy s.roy at ncl.res.in
Wed Oct 21 11:36:41 CEST 2009

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.


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

Tel.  +91 2590 2735 Office
Email s.roy at ncl.res.in

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