[gmx-users] rigid body

[Tsjerk Wassenaar]

Hi Tatiana,

As I understand it, what you basically want to do is taking HSA in a box 
of water, and subsequently calculate water-water interactions (and a 
minority of protein-protein and water-protein interactions) leaving the 
bulk of the protein-protein interactions for what they are :) . But you 
could also consider cutting on the water. If you use a molecular shaped 
box, which essentially is an optimized triclinic box, you can reduce the 
total box size for the system by half, only loosing 'irrelevant' water 
molecules. I've had a brief look at the crystal structure for HSA and it 
seems a very good candidate for such a box.

You would need to have a modified version of Gromacs to restrain the 
overall rotations (according to the method of Amadei et al., J. Chem. 
Phys. 2000 V112 p9).

At current I believe that Gromacs is still the only package that can 
handle triclinic boxes...
Might you be interested, you can just send me an e-mail...

Maybe it might be of some use.

Cheers,

Tsjerk


Tatiana Hushcha wrote:

>Dear GROMACS developers,
>
>We would like to simulate realistic behavior of the whole human serum
>albumin (HSA) molecule at the physiological conditions. We plan to use the
>modeled time characteristics of conformational transitions to interpret our
>experimental relaxation data, so the simulated times should be correct.
>
>It is our belief that the only way to solve our problem by computational
>resources available, is to treat several fragments of HSA molecule as rigid
>bodies. We studied Molecular Modeling software available, and GROMACS in
>general seems extremely attractive in view of our purposes. But we had no
>success in finding in the GROMACS User Manual the feature of treatment the
>HSA molecule as a number of rigid bodies. GROMACS Freeze Group concept would
>be of use in the case of a single rigid fragment, but employing of several
>rigid body fragments is absolutely necessary for us.
>So, we would be grateful if you give us explicit confirmation that GROMACS
>can't be used to treat a large biomolecule as a system of several rigid
>bodies. Or maybe this feature is still available? It may be not documented
>yet, for example.
>
>Looking forward to hearing from you.
>
>Best regards,
>
>Dr. Tatiana Hushcha
>Institute of Bioorganic Chemistry,
>Kiev, Ukraine
>
>
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