I prepared the supercell based on the AMBER tutorial
I have a unit cell with the box information
I tried the following
$AMBERHOME/bin/PropPDB -p unit.pdb -o supercell.pdb -ix 15 -iy 15 -iz 4
To check for the structure or overlaps I issued following command in
cpptraj script
trajin supercell.pdb
checkoverlap reportfile report.dat
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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Research Gate
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Received on Tue Aug 16 2016 - 06:30:03 PDT
