FEP: Proton of OH-Group falls on the oxygen, even if just state A is of interest
I tried to FEP a TYR to PHE by morphing OH-Proton to dummy and OH-Oxygen to
hydrogen. In EM/PR-Run/MD the proton of the OH-group falls upon the oxygen.
Tested: OPLS/AMBER-FFs, PME/CO, SOL/Vacuo. 3.2.1-tpr with 3.3.1 mdrun.
The error occured in every test with 3.3.1. It was ok with 3.2.1. It seems to be
a problem with the bonds/angles.
I set up a tripeptide in vacuo for you to make debugging easier.
#2 Updated by Berk Hess almost 14 years ago
This seems to me like a bug in grompp that I have fixed for 3.3.1.
Did you make the tpr file with 3.3 and not 3.3.1?
You probably got warnings when running grompp.
In grompp of 3.3 when the A-state parameters can be found in the defaults
and the B-state not, it gives a warning, but then uses zeros
for all parameters.
#3 Updated by Berk Hess almost 14 years ago
I just compiled 3.3.1 and grompp indeed gives the correct constraint distances.
This was a bug.
But the user should also check all warnings and get rid
of all warnings about topology stuff.
Maybe we should make grompp stop on topology warnings by default
and add a switch to continue.