[gmx-users] problems with gromacs angle restraints
spoel at xray.bmc.uu.se
Fri Nov 11 22:58:12 CET 2005
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.
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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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