[gmx-users] (no subject)
SLN Prasad Reddy
sreeyapu at rediffmail.com
Tue Jun 15 19:04:43 CEST 2004
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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
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
With many thanks in advance
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