Re: PDB file creation

From: Vermaas, Joshua (
Date: Wed Feb 08 2017 - 11:37:22 CST

Hi Matthew,

So this shouldn't actually matter. The commas are a bit suspicious though. Does the display change after you execute the $chainA moveby command? What writepdb does is take the current position as displayed on the screen and write that to the file.

Here is the error message I get when I execute your code:

$sel moveby {3, 3, 4}
atomselect moveby: non-numeric in vector

Since the moveby errors out, it doesn't actually move anything (and would be why the pieces aren't moved in the output pdb)! Instead, try something like this:

$sel moveby {3 3 4}

or alternatively

$sel moveby [list 3 3 4]


On 02/08/2017 10:26 AM, Bennion, Brian wrote:

maybe add the line:

$selection update


From:<> <><> on behalf of matthew reeves <><>
Sent: Wednesday, February 8, 2017 9:14:13 AM
To:<>; 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

> On 7 Feb 2017, at 23:52, 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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