The absolute values of the energy are meaningless. In explicit water, this
seems typical, with the elec large and negative and the vdw positive and
about 10% of elec.
you want to look at gradients, not energies, and also see if energies are
still going down. Gmax is useful too.
On Nov 10, 2015 1:22 AM, "muhammad tahir ayub" <tahirgp0.gmail.com> wrote:
> Dear Amber Users:
>
> I have minimized my apo protein in the following step
> 500 step (protein restrain 25 ) ion & WAT free
> 500 step (protein + ion restrain 25, 20 ) WAT free
> 100 step (protein + ion restrain 20, 15 ) WAT free
> 100 step (protein + ion restrain 15, 10 ) WAT free
> 100 step (protein + ion restrain 10, 5 ) WAT free
> 100 step (protein + ion restrain 5, ) ion, WAT free
> 500 step (Unrestrain system )
>
> above mentioned steps are right
> and
> what
> I got following results for 500 Unrestrained system minimization
> VDWAALS = 182243.53 EEL = -1350322.29
> 1-4 VDW = 2143.80 1-4 EEL = 22795.94
>
> should I increase the minimization step for these high value of VDW and EEL
>
> Thanks in advance
>
> Muhammad Tahir Ayub
> Junior Research Fellow
> Lab No. P-133, Computational Chemistry Unit,
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi-75270.
> Karachi-Pakistan.
> UAN: (92-21) 111-222-292 Ext. (309)
> E-mail: tahirgp0.gmail.com
> http://sites.google.com/site/zaheerqasmi/groupmember
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Received on Tue Nov 10 2015 - 03:30:04 PST
