Post date: Aug 2, 2012 3:32:49 PM
How to check if MD geometry (caused by the current parametrization) is consistent with the QM one.
Note that QM is computed in vacuo with gaussian03 and may be very slow.
module add ambertools module add gaussian antechamber -i BEN.pdb -fi pdb -o BEN.gin -fo gcrt -nc 1 -pf y # optionally add: -gm "%mem=1000MB" -gn "%nproc=8" edit BEN.gin and change the first line in… (not necessary?) #HF/6-31G* Test opt. Then:
g03 BEN.gin antechamber -i BEN.log -fi gout -o BEN-QM.pdb -fo pdb -nc 1 -pf y This gives you BEN-QM.pdb, that you should compare with the structure computed in the first step.
IMPORTANT 1. In presence of symmetry, geometry can converge to a wrong minimum. In doubt, start from non-symmetric structures (e.g. add noise)!
IMPORTANT 2. If you get “Write error in NtrExt1: Bad address” or similar: gaussian only works on mio and a few other machines due to the “va address randomization”. Ask sysadmins to disable.
Runs on 4 cores by default: 30’ for BEN on mio.
If you want to improve the parametrization of the MD structure:
xxx.frcmod file, e.g.DIHE ca-ca-c2-n3 1 1.500 000.000 4.000