[gmx-users] CHARMM to Gromacs

[Justin A. Lemkul]

Alessandro.Maiorana at roma2.infn.it wrote:
> Hi,
> I'm a physics' student of Tor Vergata university(Rome). I exploit Gromacs
> by short time. I am trying to use the CHARMM27 force field to Gromacs, but
> I have some problems. I readed your instructions from web address:
> http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,59/.
>
> I followed the procedure, that is:
> Step one: I converted CHARMM force field in ffcharmmbon.itp and
> ffcharmmnb.itp, through the use of the script
> "convert_charmm_to_gromacs.pl".
> Step two: I placed ffcharmmbon.itp and ffcharmmnb.itp in
> /usr/local/gromacs/share/gromacs/top.
> Step three: I downloaded the charmm_gromacs.tar.gz.
> Step four: I copied all files in the tar-file to
> /usr/local/gromacs/share/gromacs/top.
> Step five: I added this line "ffcharmm CHARMM 27" in FF.dat.
> Step six: The 'pdb2gmx' command was run using the command:
> "pdb2gmx -ter -f <filename>.pdb -o <filename>.gro -p <filename>.top" but
> the following error message is coming:
> Program pdb2gmx, VERSION 3.3.3
> Source code file: ter_db.c, line: 85
>
> Fatal error:
> Reading Termini Database: expected 3 items of atom data in stead of 1 on line
>        N      NH3        14.0027    -0.3000
>
> I changed the format of ffcharmm-n.tdb comparing with the ffG43a1-n.tdb,
> but the following error message is coming:
> Program pdb2gmx, VERSION 3.3.3
> Source code file: ter_db.c, line: 257
>
> Fatal error:
> Reading Termini Database: Expecting a header at line
>
>   

Can you show us the new format of your ffcharmm-n.tdb file?  I recall 
having to make some changes to mine, and I suppose you've probably just 
made a typo somewhere.  If you can paste the first entry or two of the 
.tdb file that would help.

-Justin

> Can you help me? I hope to have been clear. Thanks for the help you going
> to gave me. See you soon.
>
>
>
>
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>   

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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