[gmx-users] ligand-protein interaction using gromacs

[David Mobley]

Regarding amb2gmx.pl, it should work for converting whole systems from
Amber, but this may depend on the box geometry you are using. In
particular I think it is OK with cubic boxes but not some of the more
fancy geometries. The other option is just to convert your
protein+ligand and solvate using gromacs tools.

David


On Mon, Mar 10, 2008 at 10:31 PM, #NGUYEN CONG TRI# <NGUY0045 at ntu.edu.sg> wrote:
>
>
> 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)
> 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,
> Tri.
>
>
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