Dear All,
I have run a short TI simulation on a system using pmemd wherein, I have in one state bonded disulphide bridge (state A) and in the other unbonded bridge (State B).
The peptide I am working with is 40 residues long.
In my simulation, I have
timask1 = ':4,30',
timask2 = ':41,42',
when I extract pdb from a certain frame. I wish to make two distinct PDB for the two states.
When I replace the coordinates of residue 41, 42 with 4 and 30 respectively to get PDB of just the state B, it does not seem to work.
Can somebody kindly suggest me how do I extract pdb of the two states?
Thanks
Regards
Sowmya
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Received on Fri Jun 02 2017 - 03:30:02 PDT
