On Fri, Jan 28, 2011 at 2:14 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Jan 28, 2011, mish wrote:
>
> > I tried to do QM/MM-GBSA calculation directly over the trajectory by
> setting
> > imin = 5, maxcyc=1. I tried to the way described in one of the previous
> > post http://archive.ambermd.org/201012/0510.html
> >
> > My first snapshot seems to run fine but after that I am getting
> convergence
> > problem for SCF calculation.
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 5.7854E+17 2.6700E+17 6.0242E+19 O 16760
> >
> > BOND = ************* ANGLE = 380659.4980 DIHED =
> > 14424.2567
> > VDWAALS = ************* EEL = 163422.6168 EGB =
> > -2195805.9753
> > 1-4 VDW = ************* 1-4 EEL = -5450.7695 RESTRAINT =
> > 0.0000
> > PM3ESCF = 2227.5540
> > minimization completed, ENE= 0.57854326E+18 RMS= 0.267003E+18
> > minimizing coord set # 3
>
> This looks like a problem with the trajectory file. Was it created (say)
> by
> stripping waters using ptraj? If so, did you use the "nobox" flag on the
> trajout line?
>
> If this doesn't help, we need to find out more about how you created the
> input
> trajectory file.
>
> ...dac
>
> Thanks,
>
I used on strip :WAT to create the trajectory for this calculation. As
you suggested, also tried "nobox" but the problem remains the same. If
I visualize in the trajectory, I cant see nay weird movement or problem
with trajectory.
..mish
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Received on Sat Jan 29 2011 - 00:00:02 PST
