[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

[Yun Shi]

Hi Alan,

For example, in the Glycam_06g.dat file, you can find:
........
OH-CG-CG-OS   1   -1.10          0.0            -1
........

So this dihedral parameter has a force constant of -1.10, and this is what I
mean by "GLYCAM force field assigns negative force constants to some
dihedrals".

I did try the GMX45 approach, and using the conversion factor 4.184, I got a
difference of about 0.05%.  I am not sure if this is caused not setting step
size in the sander minimization.

Regards,
Yun







Date: Tue, 13 Sep 2011 12:03:10 +0100
From: Alan <alanwilter at gmail.com>
Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
       <CAEznbznq98PbHjdR1SMPOgdTz_pGFqsk40iZLfPQ7-NiZywJ4A at mail.gmail.com>
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Hi Yun,

Have you read http://ambermd.org/formats.html?

In particular, this note:

"""
NOTE: *the atom numbers in the following arrays that describe bonds, angles,
and dihedrals are coordinate array indexes for runtime speed. The true atom
number equals the absolute value of the number divided by three, plus one.
In the case of the dihedrals, if the fourth atom is negative, this implies
that the dihedral is an improper. If the third atom is negative, this
implies that the end group interations are to be ignored. End group
interactions are ignored, for example, in dihedrals of various ring systems
(to prevent double counting of 1-4 interactions) and in multiterm dihedrals.
*
"""

I may be failing to understand what you mean by "GLYCAM force field assigns
negative force constants to some dihedrals".

Anyway, since GMX 4.5 can go without RB convertions, you can do this:

acpype -x disac.inpcrd -p disac.prmtop --gmx45

If you have sander, you can do just one step of EM and compare against one
step EM with GMX. Do the proper conversions and Energies diff should be <
0.001%.

Cheers,

Alan

On 12 September 2011 21:21, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi all,
>
> I am not a CS person, but I did find something in acpype.py as
>
> .............
>                 if phase in [0, 180]:
>                     properDihedralsGmx45.append([
>
> item[0].atoms, phaseRaw,
> > kPhi, period])
> >                     if not self.gmx45:
> >                         if kPhi > 0: V[period] = 2 * kPhi * cal
> >                         if period == 1:
> >                             C[0] += 0.5 * V[period]
> >                             if phase == 0:
> >                                 C[1] -= 0.5 * V[period]
> >                             else:
> >                                 C[1] += 0.5 * V[period]
> >                         elif period == 2:
> > ......................
> >
> > kPhi here seems to be the dihedral force constant, and it seems if kPhi <
> > 0, no value will be assigned to C[0], C[1], C[2] ...
> >
> > I wonder if the negative dihedral force constants problem could be solved
> > by changing 'kPhi > 0' to 'kPhi != 0' for acpype?
> >
> > Thanks,
> >
> > Yun
> >
> > --
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>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
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