Your problem doesn't seem to be related to simulation but rather to how
you extract structures from the trajectory(?). You only say that "it
does not seem to work" without giving any details as to what you have
actually done e.g. what software/procedure you have been using and
what the result was. Cpptraj should be able to extract coordinates based
on a user supplied mask.
On Fri, 2 Jun 2017 10:24:48 +0000
Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> 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 - 04:00:02 PDT
