Project

General

Profile

Bug #116

FEP: Proton of OH-Group falls on the oxygen, even if just state A is of interest

Added by Maik Goette about 13 years ago. Updated about 13 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

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.

bugreport.tar.gz (935 KB) bugreport.tar.gz Small debugging testsystem Maik Goette, 11/08/2006 11:45 AM

History

#1 Updated by Maik Goette about 13 years ago

Created an attachment (id=98)
Small debugging testsystem

Tripeptide in vacuo with THR-FEP to artificial ALA/LEU-Intermediate. ;)

#2 Updated by Berk Hess about 13 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 about 13 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.

Also available in: Atom PDF