On Mon, Aug 15, 2016, Neha Gandhi wrote:
>
> There is some issue with the energies in particular vDW
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.9642E+09 4.1580E+04 5.6744E+06 HA 3277
>
> BOND = 585136.3558 ANGLE = 319433.4389 DIHED =
> 2572.6253
> VDWAALS = ************* EEL = -5610131.6247 HBOND =
> 0.0000
> 1-4 VDW = 1839.8371 1-4 EEL = 11004.4573 RESTRAINT =
> 0.0000
You have two atoms almost on top of one another in your initial structure.
Use the checkoverlap command in cpptraj to get more information. Minimization
will probably help, but be sure to use a CPU version of sander or pmemd,
not the GPU version.
Also, the initial values for the bond and angle energies are quite large:
see what happens to them upon minimization.
>
>
> When I visualise the .rst file after minimisation, it seems that the HAP
> surface is significantly changed as compared to the initial input.
Do you get a very high restraint energy? Check the output, and/or use the
ambmask utility, to make sure that your restraintmask is affecting the
atoms you want.
....dac
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Received on Mon Aug 15 2016 - 05:00:02 PDT
