Can you help me what is the format of checkoverlap command? I just have
prmtop, inpcrd and pdb files. How to use this command with these files?
Thanks
On Thu, Jun 7, 2012 at 4:49 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jun 07, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
> >
> > I am having trouble in minimization. It seems it got stuck at a point, no
> > error messages but its not moving further. Any suggestions?
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 NaN NaN 5.8908E+01 O 23176
> >
> > BOND = 446645.5044 ANGLE = 1672.6266 DIHED =
> 3358.8277
> > VDWAALS = ************* EEL = -73662.8982 EGB = NaN
> > 1-4 VDW = 999.3677 1-4 EEL = 11112.3672 RESTRAINT = 0.0000
>
> You input structure is bad, and probably has two atoms on top of each
> other.
> Use the "checkoverlap" command in ptraj to search for bad contacts.
>
> ....dac
>
>
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Received on Thu Jun 07 2012 - 22:30:03 PDT
