On Tue, Aug 16, 2016 at 7:17 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> To check for the structure or overlaps I issued following command in
> cpptraj script
>
> trajin supercell.pdb
> checkoverlap reportfile report.dat
>
You'll want to run the 'check' command on the actual topology and
restart that gives you the strange energies, not the PDB.
-Dan
> Alternatively I also performed check command after loading supercell.pdb in
> the tleap file.
>
> No information on steric clashes/overlaps were reported. I also visulaised
> the structure in Discovery studio and no clashes/overlaps were found.
>
> I tested a smaller cell 2x2x2 using same method above and I manually
> increase the box size in the inpcrd file as compared to the one assigned by
> tleap. This successfully finished minimization. I will try changing box
> size of supercell tomorrow and see if it can successfully run.
>
> Cheers,
> Neha
>
>
>
>
> On 16 August 2016 at 22:04, David A Case <david.case.rutgers.edu> wrote:
>
>> On Tue, Aug 16, 2016, Neha Gandhi wrote:
>>
>> > I did minimization on a unit cell of HAP. It works fine with or without
>> > restraints. The trouble starts when I prepare a supercell 15x15x4 size.
>>
>> What, exactly, did you do to "prepare a supercell 15x15x4 size"?
>>
>> Also, how, exactly, did you you conclude that there were no overlaps in
>> your
>> structure?
>>
>> Remember to try to report exactly what you did (what the commands were,
>> what
>> the results were). What you have been reporting is what you intended
>> to do, which might not (in this case: probably does not) correspond with
>> what
>> you actually did.
>>
>> ...dac
>>
>>
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>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Tue Aug 16 2016 - 08:00:06 PDT
