Hi
Try the -ff option of pdb2gmx, if you're not able to get it working.
This less complicated.
pdb2gmx -f pdb.pdb -ff ffG43a1
Should work
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Mitra Kheirabadi wrote:
Dear Dr.Periole
I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but
sorry again I did not appear. please help me.
Respectfully
*/Mitra Kheirabadi <[EMAIL PROTECTED]>/* wrote:
Dear Periola
I appreciate your kindly help.
Respectfully
*/Xavier Periole <[EMAIL PROTECTED]>/* wrote:
On Tue, 8 Jan 2008 06:35:28 -0800 (PST)
Mitra Kheirabadi wrote:
> Dear Dr. Smith
>
> I want to run a virus phosphorylated protein by gromacs.
Furtunatly, you
>construct related force field by ffG43A1p name. I copied this
force field to
>top. file gromacs but when I constructed pdbgmx, there is no
any ffG43a1p to
>select. Could you help me?
> I be so grateful to receive any information about it.
you must modify the file top/FF.dat and include the new force field.
XAvier
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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