Thanks for promptly replying Jason.
Below my comments/answers.
On 10 July 2014 20:13, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Jul 10, 2014, at 10:59 AM, Massimiliano Porrini <mozz76.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am having some troubles with the module sander.
> >
> > If I use sander of AT14 for executing a minimisation,
> > I obtain the following "nice" energy breakdown:
> >
> > BOND = 30.4484 ANGLE = 188.7898 DIHED =
> 113.9438
> > VDWAALS = ************* EEL = 409.0441 EGB =
> 0.0000
> > 1-4 VDW = 53.2129 1-4 EEL = -1105.5194 RESTRAINT =
> 0.0000
> >
> > where the high VDW energy is simply due to some atom clashes.
> >
> >
> > Whereas if I feed sander of either Amber11 or Amber12 with
> > exactly the same topology and coordinates files I obtain different
> values only
> > for the 1-4 VDW and EEL energies (which are *Not a Number* and
> > *-Inf* respectively):
> >
> > BOND = 30.4484 ANGLE = 188.7898 DIHED =
> 113.9438
> > VDWAALS = ************* EEL = 409.0441 EGB =
> 0.0000
> > 1-4 VDW = NaN 1-4 EEL = -Infinity RESTRAINT =
> 0.0000
> >
> > Since my molecule is a modified residue, hence
> > I would like to make sure that I'm
> > correctly treating the system.
> >
> > Does anybody have any explanation for this behaviour?
>
> It's possible that your topology files and structures are incompatible
> (this should be readily obvious if you visualize your molecule using the
> prmtop and inpcrd files).
If I visualise my topology and coordinates files they look fine: except
from two hydrogen
atoms which clash with two other hydrogen atoms, and this gives rise to the
high VDW energy contribution
(confirmed by "checkoverlap" command in cpptraj).
It's also possible that your periodic box is not defined correctly, so
> periodic images are overlapping with other atoms in the unit cell.
>
I am not using PBC, the minimisation was run in vacuo and here I reported
only
the first step, just to show the difference between Amber1[1,2] sander and
AmberTools14 sander.
As I understood, somehow this difference might be in how *sanders*
interpret the 1-4 interactions, which result to be
NaN and -Infinity with sander of Amber1[1,2].
Indeed, the minimisation runs smoothly with AT14 sander and terminates by
getting rid of the aforesaid
clashes between hydrogen atoms, whereas it stops using Amber11 or Amber12
sander
because of the 1-4 interactions values.
I need to add that in the modellisation of my modified residues, I included
a torsion potential.
But I wonder why "it works" fine with AT14 sander and it does not with the
other two sanders.
> You can use the "checkoverlaps" command in cpptraj to look for the clashes
> that are causing problems. That should help you diagnose what is happening.
>
> Good luck,
> Jason
>
Thanks again for your time.
Max
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Dr Massimiliano Porrini
Valérie Gabelica Team
U869 ARNA - Inserm / Bordeaux University
Institut Européen de Chimie et Biologie (IECB)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 63 31
http://www.iecb.u-bordeaux.fr/teams/GABELICA
Emails: m.porrini.iecb.u-bordeaux.fr
mozz76.gmail.com
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Received on Fri Jul 11 2014 - 04:00:02 PDT
