[gmx-users] ligand-protein interaction using gromacs

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 11 11:10:31 CET 2008

Quoting #NGUYEN CONG TRI# <NGUY0045 at ntu.edu.sg>:

> 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?

It is likely due to bad contacts.  Check the list archives for relevant
discussions (there are many).  Try a thorough energy-minimization of your
system to relax bad contacts.


> Is there anyone experienced in this problem, could you please give me some
> advice, I really appreciate.
> Best regards,
> Tri.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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