Jamie Seyed wrote:
Hi Justin,
I used opls and I already tried PRODRG, but it did not help... I
What force field are you trying to use for your simulation?
appreciate if you give the address of the related page of the website??
From the homepage: Downloads -> User Contributions -> Other software
because I really problems to open some parts of the gromacs website. If
non of them help, should I use molden myself to find all the entries???
I don't know what you mean. However you assign parameters must be consistent
with the original derivation of the force field. Whether or not you can do that
in molden, I don't know.
Between PRODRG and the contributed scripts, you should be able to write
toplogies for Gromos, OPLS, and AMBER.
-Justin
Thank you very much for any suggestion.
On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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