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

[gportel at gwdg.de]

Hi Alan,

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,

Guillem


Alan wrote:
> 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-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