[gmx-users] problems with gromacs angle restraints

[David Mobley]

David,

I'm not using FEP in these calculations.

Looking at these routines they look fine, but I'm wondering where
pdihs.phiA and pdihs.phiB are set. My suspicion is that either (a)
they are converted from degrees into radians twice (as this conversion
happens once in the dopdihs_min routine, and possibly also when
they're first set), or (b) they are never set and thus assumed zero.

I haven't been able to find where these are set for the F_ANGRES case.
I have to admit I'm a bit of a novice to the code, but it looks like
they're set for F_ANGRESZ in convparm.c, but the case statement there
for F_ANGRES is empty. In fact, I can't find a case statement anywhere
in the code for F_ANGRES which does anything. There are just a bunch
of empty case statements. (i.e. "grep -r F_ANGRES *" in the src
directory only turns up empty case statements. Is this the problem?

If you can't help me out here, I'll know a little more later, because
I'm trying a couple test runs where I vary the preferred angle
drastically to see if it makes any difference in the restraining
energies I'm getting.

Thanks,
David




On 11/11/05, David <spoel at xray.bmc.uu.se> wrote:
> On Fri, 2005-11-11 at 13:23 -0800, David Mobley wrote:
> > Dear all,
> >
> > I'm hoping someone can take a look at the source code for computing
> > angle restraint energies, or direct  me to where to look in the source
> > code. I'm particularly interested in making sure that angle restraints
> > are functioning as advertized in the manual.
> >
> > Here's the situation:
> > I have a system with a small molecule in a binding site in the
> > protein. I'm trying to impose distance, dihedral, and angle restraints
> > to restrain the orientation of the small molecule relative to the
> > protein. I'm computing the free energy for turning these on, but never
> > mind that. I've previously done the calculations in AMBER and am now
> > doing them in GROMACS with the AMBER ff. Distance and dihedral
> > restraints are working as I expect, but angle restraints are not.
> > Particularly, the if I begin a calculation with the small molecule
> > having a particular set of angles according to g_angle, then impose
> > angle restraints to keep it there, at the end of the restrained
> > calculation the angle restraints have forced the ligand AWAY from its
> > initial orientation, at a considerable energetic cost.
> >
> > My guess is that either:
> > (a) The preferred angle read from the topology file is being
> > interpreted as being in radians even though it should be in degrees
> > (to be consistent with the dihedral restraint format), or
> > (b) the functional form being used for angle restraints is NOT that
> > given around p. 64 of the manual.
> >
> > I haven't been able to find the relevant section of code. Can someone
> > either direct me to it or check?
> >
> > FYI, here, I'm using angle restraints where (see p. 64) I'm computing
> > the angle ABBC (so atom k is identical to atom l) because I want to
> > restrain the angle ABC. According to the functional form given in the
> > manual this should work, but if in fact GROMACS is doing something
> > different than what's in the manual it might not work.
>
> Check routines do_pdihsmin and angres in src/gmxlib/bondfree.c
> It might well be that there recently was a bug fix in this bit of the
> code in case you are using free energy calculations. Without FEP it
> should be fine.
>
> >
> > Thanks,
> > David
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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