[gmx-users] Re: converting parmbsc0 dihedrals to RB function

Alan alanwilter at gmail.com
Fri Apr 9 11:29:50 CEST 2010

Hi Guillem,

Many thanks for your clarification. I was lazy to find out and remember why
psc0 was not ported to GMX by ffAmber previously and it was exactly because
what you've said.

And because I was not confident enough, I didn't implement that for acpypi,
which I believe does better than amb2gmx in general, so I would be glad if
you could take a look at it and if you could let me know which modifications
you did to amb2gmx.

I am taking plunge in this problem again and I'll try to come out with a
solution based in what you suggest.



On Fri, Apr 9, 2010 at 00:53, <gmx-users-request at gromacs.org> wrote:

> Right, the only dihedral angles that do not allow an exact translation to
> RB because of the phase are the ones involving the new parametrization for
> nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
> populations of states right, thus avoiding the loss of helicity on the
> long run. For proteins, there's no difference at all, so you can use
> ffamber.
> I've used the combined approach you mention without problems. The only
> thing is that I do not use pdb2gmx. Rather I use amber's tools
> (leap+libraries, all free in ambertools) to get a topology, and then I use
> a slightly modified version of amb2gmx.pl script to get a gromacs
> topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase
> does not allow a direct conversion to RB form. Typically you have three
> entries for the same dihedral, this is no problem at the itp level, grompp
> captures them all. With this approach I reproduced a torsional scan of
> parmbsc0 from amber md tool using gromacs, so I feel confident about it.
> Another option is to use the ffamber parameters and change the itp file
> including the new ones.
> I should also mention that I had problems importing the new dihedrals
> using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if
> type 1 or 3 is used. There was a new dihedral type that could be used in
> the development versions, but... for a reason it did not work out for me,
> don't recall exactly why. It could well be that it would have worked with
> more patience from my side.
> Hope this helped, somehow. You were on the right direction anyway.
> best,
> Guillem

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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