From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Feb 08 2017 - 08:46:20 CST
Hi Matthew,
That sounds odd. Could you post the script/commands you used to
translate/rotate the molecules and save the pdb?
On Tue, Feb 7, 2017 at 6:52 PM, matthew reeves <mreeves94_at_gmail.com> wrote:
> Hi,
>
> I’m preparing to run a namd simulation on a growth hormone bound to a
> receptor to see how the energy evolves with time. I am able to isolate each
> of the two chains in the molecule but I need them at a set distance away
> from each other before starting the simulation.
>
> I seem to be having trouble creating the necessary PDB file for the whole
> system after I have set the two chains at the desired distance apart (after
> translation, rotation etc.). The ‘writepdb’ command doesn’t seem to work in
> this scenario but rather produces a PDB file that returns the two chains to
> their original position.
>
> Is there any way that a separate PDB file can be created for the final
> positions of the chains? Any advice would be greatly appreciated.
>
> Regards
> Matthew.
>
>
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