Re: Fixed atoms.

From: Maxim Belkin (
Date: Thu Jun 05 2014 - 17:14:48 CDT

You can do it easily in VMD with a simple script like this:

mol load pdb pdbfile.pdb
set all [atomselect top "all"]
set sel [atomselect top "<YOUR SELECTION FOR CARBON ATOMS - CHANGE THIS>"]
$all set beta 0
$sel set beta 1
$all writepdb pdbfile_beta_1.pdb

$all delete
$sel delete
mol delete top

On Jun 5, 2014, at 5:03 PM, Aron Broom <> wrote:

> I don't think anyone uses a particular software, you're just changing a text value. You just need to use a text editor that isn't garbage (or probably most people write a quick python or bash script). I'm guessing you are on Windows? There are windows versions of decent linux editors, but there are also native-windows editors like that are good editors that won't mangle the files.
> You only change the beta values of the atoms you want to fix, so just only change the carbon atoms beta-values... It almost sounds like you were trying to change ALL the beta values, which would make for pretty static dynamics.
> But really, if you are in the business of doing MD, you should invest the time in learning a simple scripting language, the most popular at the moment being python, and then you can write some quick code to automate this task for you. It's difficult to overstate the benefits of having at least some minor coding ability and understanding.
> On Thu, Jun 5, 2014 at 5:15 PM, Gurpreet Kaur Dhindsa <> wrote:
> Dear all,
> I want to fix atoms in my simulation. By reading the blogs, they said I have to change the
> 'B' value from 0 to 1 to fix the atoms. Can you please guide me what software can do this?
> I tried with textpad but it changed the format of pdb. The other thing, my system contains water
> and carbon. I want to fix carbon only. Please tell me what commands should I use to fix the
> carbon atoms.
> Thanks,
> G
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

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