Re: [AMBER] solid surface simulation in amber

From: Neha Gandhi <>
Date: Tue, 16 Aug 2016 23:17:47 +1000

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.


On 16 August 2016 at 22:04, David A Case <> 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
> _______________________________________________
> AMBER mailing list

Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
AMBER mailing list
Received on Tue Aug 16 2016 - 06:30:03 PDT
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