From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
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]
-Josh
On 02/08/2017 10:26 AM, Bennion, Brian wrote:
maybe add the line:
$selection update
brian
________________________________
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu><mailto:owner-namd-l_at_ks.uiuc.edu> on behalf of matthew reeves <mreeves94_at_gmail.com><mailto:mreeves94_at_gmail.com>
Sent: Wednesday, February 8, 2017 9:14:13 AM
To: namd-l_at_ks.uiuc.edu<mailto: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><mailto: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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