[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

vivek sharma viveksharma.iitb at gmail.com
Mon Jan 25 08:04:21 CET 2010

Hi All,
 I was trying *GROMACS Tutorial for Drug – Enzyme Complex* by *John E.
Kerrigan* over one docked complex in following way.
I generated topology and gromacs co-ordinates for ligand and cofactor
successfully using PRODRG beta.
Protein file is processed through "pdb2gmax_d" and resulted .gro and .top
files are modified with PRODRG output (keeping *Chirality- yes, **Charges-full,
EM-No*) as instructed in tutorial.
Now when I am processing the modified .gro file to generate box, the ligand
and cofactor are going away from the protein molecule and I am not able to
analyze the complex.
Can anybody help me to find the reason for this situation, Is it because of
PRODRG options or something else?

If it i sbecause of modified co-ordinates from PRODRG, how can i keep the
co-ordinates unchanged?

I have done same exercise successfully with other molecules earlier.

Any help or experience regarding this problem is highly appreciated.

With tHanks,
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