AW: stereo-chemical inversion during MD

From: Norman Geist (
Date: Tue May 08 2012 - 01:01:05 CDT

Hi Gordon,


I’m not a specialist for biochemistry, but what you say could make sense as the minimization looks for the best energy conformation. It could be, that this angle is a better energy conformation for a particular system. But when it’s bounded to other residues, it would maybe interfere with other side chains and so would stay with the original angle. That would be easy to try out. I can hardly imagine that the minimization algorithm can work against the FF parameters.


Norman Geist.


Von: [] Im Auftrag von Gordon Wells
Gesendet: Montag, 7. Mai 2012 19:01
Betreff: namd-l: stereo-chemical inversion during MD


Hi All


I've encountered a strange situation when simulating a particular conformation of L-Glu. During minimisation the bond angle between the carboxyl-C, C-alpha and amino-N decreases from 112° to 89°. When this is subsequently used for MD there is often a stereo-chemical inversion around the C-alpha. I see this when simulating the system in its original protein complex and free in solution (TIP3 solvent for both).


I can prevent it by using a very short minimisation (50 instead of 1000 steps), increasing the di-electric or decreasing the partial charges on the ammonium hydrogens. Nonetheless, I'm sure this strained conformation shouldn't be produced in the first place (I'm not able to replicate this behaviour in macromodal or desmond) The force between the carboxyl oxygen (nearest to the ammonium moiety) and the ammonium hydrogens seems to be too high.


I've attached before and after pdbs of the free L-glu. I get the distorted conformation from the following namd input (with and without pbc):


coordinates LGlu_autopsf.pdb

structure LGlu_autopsf.psf


paratypecharmm on

parameters par_all27_prot_lipid_na.inp


outputname minall-lglu-only

binaryoutput yes

outputenergies 25


switching on

cutoff 12

switchdist 10

pairlistdist 14

exclude 1-4


fixedAtoms off


numsteps 1000

dielectric 1

minimization on


Is this forcefield related, bad input file or possibly a bug in NAMD?

-- max(∫(εὐδαιμονία)dt)

Dr Gordon Wells
Chemistry Department

Emory University

Atlanta, Georgia, USA


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