sir I tried it for 500 step minimization and its ended normally now.
On Tue, Nov 28, 2017 at 6:44 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Nov 28, 2017, Rana Rehan Khalid wrote:
> >
> > I want to minimize the structure but when simulation start the values of
> > VDWAALS not show. is it due to poor starting structure or structure have
> > more clashes. KIndly tell hoe i can remove the clashes through MD
> > simulation. Regards
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 3.3484E+18 9.6235E+17 4.9465E+20 C 6484
> >
> > BOND = 5320.4918 ANGLE = 24456.6551 DIHED =
> > 20708.3171
> > VDWAALS = ************* EEL = -645997.9707 HBOND =
> > 0.0000
> > 1-4 VDW = ************* 1-4 EEL = 56119.7849 RESTRAINT =
> > 0.0000
>
> You have two atoms almost of top of one another. (The "****" means
> the number is too big to fit in the space provided.) You can use the
> "checkoverlap" command in cpptraj to locate these.
>
> If there only a small number of such clashes, minimization will often solve
> the problem: try 100 steps of minimization, and print at every step
> (ntpr=1).
> If you are lucky, you will arrive at a useful structure. If not, you will
> have to figure out a way to get a better starting structure.
>
> ....dac
>
>
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Received on Tue Nov 28 2017 - 06:30:03 PST
