On Tue, Oct 18, 2016, vadiraj kurdekar wrote:
>
> from this when I perform equilibration with NPT with restraining the
> complex with 100 kCal, I see a drifting of complex to the centre of
> PBC. I observed that protein and peptide are drifting at different rate
> leading loss of original conformation.
It's hard to tell what you are restraining, since we don't know which residues
you consider to belong to the "protein" and which to the "peptide". The
comments in your input file suggest that you are only restaining the protein,
so "loss of the original conformation" would be expected.
The "drifting of complex to the center of the PBC" would be expected if you
use iwrap=1. Turn that off (and set ntxo=2 for Amber versions before
Amber16.)
...hope this helps....dac
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Received on Tue Oct 18 2016 - 06:00:05 PDT
