Re: PDB file creation

From: Chitrak Gupta (
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 <> 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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