[gmx-users] Re: Request

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 21 14:18:22 CEST 2009

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.


> Regards,
> Gromacs user in need
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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


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