[gmx-users] charmm to gromacs

Jernej Zidar jernej.zidar at gmail.com
Tue Dec 2 07:47:50 CET 2014

Dear Rebeca,
  For small organic molecules you should use the portal
www.paramchem.org to do the initial atom typing. Then you can use the
python script found on the website of dr MacKerell
(http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) to convert
the resulting str file to a Gromacs-friendly format (including writing
the top and itp files).


On Tue, Dec 2, 2014 at 2:17 PM,
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> On 12/1/14 10:49 AM, Rebeca Garc?a Fandi?o wrote:
>> Dear users,
>> I am trying to generate .itp files for simulating a small molecule in GROMACS using the CHARMM force field.
>> Starting from a pdb, and using MATCH
>> MATCH.pl -forcefield top_all36_cgenff test.pdb
>> I obtain 3 files: test.rtf, top_test.rtf and test.prm
>>  From these files, I would like to obtain the .itp files for gromacs, and for that, I have tested the sript "charmm2gromacs-pvm.py"
>> ./charmm2gromacs-pvm.py test.prm top_test.rtf
>> This created a folder called cgenff-2b7.ff with 6 files:
>> aminoacids.rtp  atomtypes.atp  ffbonded.itp  ffnonbonded.itp  forcefield.doc  forcefield.itp
>> However, these files are empty :-(
>> Could anyone help me, please?

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