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). It's also possible that your periodic box is not defined correctly, so periodic images are overlapping with other atoms in the unit cell.
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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 10 2014 - 11:30:03 PDT
