[gmx-users] Re: pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs (Tsjerk Wassenaar)
ploetz at ksu.edu
Wed Nov 23 19:08:07 CET 2011
Thank you for your advice! grompp does not complain (with all three of
the previously mentioned versions of GROMACS), but the processed topology,
processed.top, also does not have the terms filled in, as I show below for the
[ bonds ]
; ai aj funct c0 c1 c2 c3
56 57 2 0.1830 5.6200e+06
57 585 2
58 59 2 0.1230 1.6600e+07
(This is also true for the angles and dihedrals.)
But, I ran some minimization and 100 ps of equilibration (with no position
restraints) and viewed the output using Gromacs's ngmx trajectory viewer so
that bonds would be drawn based upon the topology and not the proximity of atoms
(what e.g., Rasmol does). There does appear to be three disulfide bonds present.
I then used g_dist to calculate the distance between the two sulfur atoms
in each of the disulfides during that short equilibration. They all came out on
average to be 0.2040 nm, which is exactly what the equilibrium bond length would
be if it were using the correct bond type.
So, while it seems strange to me that they do not appear in the topology
(preprocessed or processed), I am reassured that GROMACS really is using
the disulfide information with the GROMOS FFs.
I appreciate your help.
These missing terms are filled in automatically by grompp from the
bondtypes, angletypes and dihedraltypes definitions in the *bon.itp.
Unless grompp complains about missing terms, you'll be fine. You can
check whether everything is okay by writing out a processed topology
(grompp -pp) and looking up the bonds.angles/dihedrals there.
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