Re: PDB file creation

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Feb 08 2017 - 11:27:29 CST

Hi Matthew,

Yes, updating the selection might help. Also, have you made sure your
"$chainA" was defined correctly?

Chitrak.

On Wed, Feb 8, 2017 at 12:23 PM, Bennion, Brian <bennion1_at_llnl.gov> wrote:

> maybe add the line:
>
> $selection update
>
>
> brian
>
>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> matthew reeves <mreeves94_at_gmail.com>
> *Sent:* Wednesday, February 8, 2017 9:14:13 AM
> *To:* namd-l_at_ks.uiuc.edu; matthew reeves
> *Subject:* Re: namd-l: PDB file creation
>
> Hi Chitrak,
>
> Yes of course, thanks for the reply.
>
> I isolated the two parts of the molecule and defined the growth hormone as
> ‘chainA’ and the receptor as ‘chainB’. This is along the lines of what I
> typed in the Tk console
>
> $chainA moveby {3, 3, 4}
> set selection [atomselect top “all”] (selection including both parts
> of the chain)
> $selection writepdb updated.pdb
>
> When I then checked the ‘updated’ PDB file, chains A and B were then in
> their original positions, as if they hadn’t even been translated. Is there
> an alternative way I can do this?
>
> Best wishes
> Matthew
>
>
>
> > On 7 Feb 2017, at 23:52, 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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