Fwd: Re: AW: stereo-chemical inversion during MD

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue May 08 2012 - 03:26:25 CDT

Stereochemical inversion implies bond breaking and bond making, and this
is not possible by molecular dynamics and using all atoms force fields.
It is advisable to carefully check your input PDB file, residue name,
atoms etc.

On 5/8/2012 8:01 AM, Norman Geist wrote:
>
> 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:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Gordon Wells
> *Gesendet:* Montag, 7. Mai 2012 19:01
> *An:* namd-l_at_ks.uiuc.edu
> *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(?(??????????)dt)
>
> Dr Gordon Wells
> Chemistry Department
>
> Emory University
>
> Atlanta, Georgia, USA
>
>
>
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