[gmx-users] Convert drug Charmm topology to Gromacs

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 24 18:37:44 CEST 2011

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.


> Steve
> On Wed, Aug 24, 2011 at 3:57 PM, Jianguo Li <ljggmx at yahoo.com.sg 
> <mailto:ljggmx at 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.neumann08 at gmail.com
>     <mailto:s.neumann08 at gmail.com>>
>     *To:* gmx-users at gromacs.org <mailto:gmx-users at 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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