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<BR>
<BR>
Hello gromacs users<BR>
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<BR>
<BR>
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.<BR>
<BR>
2. I processed protein file alone with pdb2gmx<BR>
3. Appended DRGFIN.gro at the end of protein.gro<BR>
4. Then edited protein.top as follows<BR>
- add #include "atp.itp" after the force field parameter<BR>
- Under [molecules] section : add ATP under compound and <BR>
2 under #mols.<BR>
<BR>
Then i processed with following commands<BR>
<BR>
- editconf<BR>
- genbox<BR>
I am successful with these two commands<BR>
<BR>
But when i used grommp command it is giving fallowing error<BR>
Fatal error: Invalid order for directive atoms, file ""atp.itp"",line 1<BR>
<BR>
Kindly suggest me a solution for this problem<BR>
<BR>
With many thanks in advance<BR>
<BR>
Prasad reddy<BR>
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