[gmx-users] ligand-protein interaction using gromacs

#NGUYEN CONG TRI# NGUY0045 at ntu.edu.sg
Tue Mar 11 07:31:58 CET 2008

Dear all,
I'm trying to study the interaction between NADH and a protein. And because the parameters for NADH have been developed in amber99 and amber94 force fields, so I just used the contributed parameter files for my simulation. The coordinates I got from docking results.
I made my whole system, including the protein and ligand in amber, and generated, say complex.inpcrd and complex.prmtop. Then I used the distributed amb2gmx.pl distributed elsewhere to convert them into complex.gro and complex.top. It seems to be work well. But I'm not sure whether it is appropriate to do that because my system is very big (the protein with 5000 atoms and NADH 71 atoms, plus solvent). I notice that amb2gmx.pl was only tested for small molecules. 
One more thing, I tried to run the minimization but maybe there is very close contact between the ligand and the protein so the minimization failed. The close contact maybe due to the added hydrogen atoms by amber, which were trimed away upon docking.  
Below is the error:
Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ]
Please report this to the mailing list (gmx-users at gromacs.org <mailto:gmx-users at gromacs.org> )
Does the problem comes from close contact between NADH and the protein or anything else? If it the case, then what should I do, because I cannot arbitrarily re-position the ligand, can I?
Is there anyone experienced in this problem, could you please give me some advice, I really appreciate.
Best regards,
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