[gmx-users] problems with gromacs angle restraints
spoel at xray.bmc.uu.se
Sat Nov 12 10:10:32 CET 2005
On Fri, 2005-11-11 at 15:17 -0800, David Mobley wrote:
> 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.
Have you checked the tpr file with gmxdump -s topol.tpr | less
Search for ANGR
> 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?
These are not empty case statements, but rather the control flow of the
program "fall through", i.e. all three are treated like dihedrals.
There is no conversion here, that means that if you define the angle
restraints in degrees in the top file it *should* be fine.
> 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.
> 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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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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