Steven Neumann wrote:
Hi,
Thank you for the information.
Is it easier just to use SwissParam as mentioned and straight obtain itp
file for my drug?
I'd say so. Otherwise you have to go through the trouble of converting it all
into the proper format and units. Writing an .rtp entry is just as much work as
writing an .itp file (more or less), and pdb2gmx really isn't meant for
standalone molecules, because then you'll have to do a bit more (trivial)
cleanup to make the resulting .top an .itp file.
If you have the means to produce a reasonable .itp file directly, do so.
-Justin
Steve
On Wed, Aug 24, 2011 at 3:57 PM, Jianguo Li <ljg...@yahoo.com.sg
<mailto:ljg...@yahoo.com.sg>> wrote:
Hi,
The .str file contains the information of atomtype, bonds
and improper dihedrals, so it is eneough to write a .rtp file. Then
using pdb2gmx to generate the itp file.
And you also need to add the missing parameters from CgenFF into the
itp parameter files based on chapter 5, as Justin suggested.
best regards,
Jianguo
------------------------------------------------------------------------
*From:* Steven Neumann <s.neuman...@gmail.com
<mailto:s.neuman...@gmail.com>>
*To:* gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
*Sent:* Wednesday, 24 August 2011 20:26:13
*Subject:* [gmx-users] Convert drug Charmm topology to Gromacs
Dear Gromacs Users,
I have generated topology file for CHARMM ff using online server for
my small molecule (I obtained .str file). How can I convert it into
the Gromacs topology file (.itp)?
Thanks,
Steve
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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