[gmx-users] Re: Request

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I do not 
offer free private tutoring :)

nikhil damle wrote:
> Hi,
> 
>     GROMACS-3.3.3 provides ATP in the .rtp file of ffG43a1 force field. 
> But it is not recognized as the protein residue. So then how to carry 
> out MD simulation of a protein with ATP non-covalently bound in ATP 
> binding pocket ? Unfortunately as the GROMACS site is not working, I am 
> unable to find the .itp file which can be included in .top file of the 
> protein. I will be grateful if got the help as soon as possible.
> 

If there is an .rtp entry, simply run your structure through pdb2gmx.  If you 
run into problems from there, post a message to the list.

-Justin

> Regards,
> Gromacs user in need
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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