From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue May 08 2012 - 04:53:27 CDT
Gordon,
Your 'distorted' PDB structure, enclosed in attachment, comprises of two
identical overlapped residues having something differently positioned
atom (open this file by the lister and see), just I have no idea how
you obtain this file. Try to check initial PSF file. Even in this file
stereochemistry is the same as in the input file. Also if you perform
calculation for one residue, why this is residue 2002?
Branko
On 5/7/2012 7:01 PM, Gordon Wells wrote:
> 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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