[gmx-users] Re: converting parmbsc0 dihedrals to RB function
gportel at gwdg.de
gportel at gwdg.de
Fri Apr 9 11:43:05 CEST 2010
I have no experience with acpypi, so I can't tell which one does better,
or why... rdparm not being needed, that would be a strong point.
Unfortunately, I'm running a bit short of time at the moment, so I can't
really spend a lot of time looking into unknown codes, hope you
understand... Nevertheless, the modifications are straightforward : if the
phase of the dihedral in question is different than 0 or 180, then you
should print the 3 dihedrals as type 1 - and converting the units -,
instead of combining them as RB. I did not do anything else to amb2gmx.
best of luck,
> 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
> RB because of the phase are the ones involving the new
> nucleic acids. Namely, it corrects the alpha/gamma transitions to
> 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
> 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
> 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
> 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,
> captures them all. With this approach I reproduced a torsional scan of
> parmbsc0 from amber md tool using gromacs, so I feel confident about
> 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
> type 1 or 3 is used. There was a new dihedral type that could be
> the development versions, but... for a reason it did not work out
> don't recall exactly why. It could well be that it would have worked
> more patience from my side.
> Hope this helped, somehow. You were on the right direction anyway.
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