VMD-L Mailing List

From: Hannes Loeffler (Hannes.Loeffler_at_stfc.ac.uk)
Date: Fri Nov 08 2013 - 03:27:34 CST

On Fri, 8 Nov 2013 08:09:33 +0100
Spitaleri Andrea <spitaleri.andrea_at_hsr.it> wrote:

> Hi,
> we recently published a protocol to use gromacs trajectory to
> calculate MM/PBSA. You may think to convert dcd to trr/xtc and try it.
>
> let me know if you want it
>
> http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046902

That's nice but you should probably also point out that the trajectory
format is not really the issue here. Those can readily be converted by
various tools.

The question is how to deal with the chosen force field. If it is one
of the AMBER ones, the OP doesn't quite say, than the AmberTools are
probably the best bet for doing the MM-PBSA analysis.

If the force field is CHARMM then there may be a bumpy road ahead. I
know GROMACS handles CHARMM force fields just fine but the OP first
needs to generate topology files compatible with the originally
generated one (or the original trajectory). It would be useful to know
how this can be achieved.

In any case, the GROMACS route sounds interesting esp. since GROMACS is
available for free. But it would be good to have a user friendly
solution too.

Cheers,
Hannes. 

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