On Thu, May 31, 2018, Aashish Bhatt wrote:
>
> I need to perform dynamics for a protein complex. For this i tried making
> the topology and coordinate file. When i visualized topology file and pdb
> file in VMD, Dimensions of the box are not cubic(attached files).
I see two issues here:
1. The solvateBox command will not make a cubic system, but rather a
rectangular parallelopiped (hope that's the right term!), with different
lengths on each side. (Maybe that is what you meant.)
2. The VMD visualization problem comes from limitations in the old PDB
format, which cannot (easily) describe more than 100,000 atoms or 10,000
residues. The are various non-standard workarounds to this problem, and
VMD seems not to recognize what Amber does.
Try loading the prmtop and and initial coordinate (restart) file into
VMD.
...good luck...dac
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Received on Thu May 31 2018 - 04:30:02 PDT
