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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--
========================================
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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