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. Cheers, Alan On Fri, Apr 9, 2010 at 00:53, <gmx-users-requ...@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. >>http://www.bio.cam.ac.uk/~awd28<<
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