[gmx-users] (no subject)
spoel at xray.bmc.uu.se
Tue Jun 15 21:40:32 CEST 2004
On Tue, 2004-06-15 at 19:04, SLN Prasad Reddy wrote:
> Hello gromacs users
> I am trying to run md-simulation on a protein having ATP. I could not run "pdb2gmx" with a protein having ATP. Then i was told by gromacs user to use prodrg. I followed a tutorial by name DRUG-Enzyme complex of Gromacs and i did as follows
> 1.I submitted atp file alone to prodrg and if has given many out-put files from them i used DRGGMX.itp (renamed to atp.itp) and DRGFIN.gro for futher use.
> 2. I processed protein file alone with pdb2gmx
> 3. Appended DRGFIN.gro at the end of protein.gro
> 4. Then edited protein.top as follows
> - add #include "atp.itp" after the force field parameter
> - Under [molecules] section : add ATP under compound and
> 2 under #mols.
> Then i processed with following commands
> - editconf
> - genbox
> I am successful with these two commands
> But when i used grommp command it is giving fallowing error
> Fatal error: Invalid order for directive atoms, file ""atp.itp"",line 1
> Kindly suggest me a solution for this problem
look in atp.itp on line 1, and remove the force field inclusion
statement. it is already in your protein.
> With many thanks in advance
> Prasad reddy
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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