Jamie Seyed wrote:
Dear gmx users,
I need some help for generating a itp file for my molecular structure. I
am using molden and now I have the xyz and pdb files. I read through
mailing list but seems I should provide itp myself. But I don't know the
right way to do that. Is it using molden and find one-by-one bond sand
angles and dihedrals... . If I have already the itp file for a part of
molecule is it only to add the information of new atoms to the old itp
file?? I will really appreciate it if someone gives me better ideas and
more related information to make my itp file.
Depending on the force field you want to use, there are various scripts in the
User Contributions section of the Gromacs site. The PRODRG server is also
useful for generating an initial topology, but the charges and charge groups it
assigns are often unsatisfactory and require manual adjustment.
-Justin
Many Thanks in Advance,
Jamie
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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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