VMD-L Mailing List

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Fri Jul 26 2013 - 12:55:36 CDT

Revathi,

The change from the cgenff codes to the 3-letter versions that NAMD/VMD
prefers is something you will need to do manually. If you have a text
editor like emacs, you simply need to choose a reasonable abbreviated
version of the cgenff and use the "replace-string" option that is very
useful in emacs. For example, I may want to change the CG2O3 atom type to
simply read CO3, and I would simply replace each instance of CG2O3 with
CO3. It's unlikely you'll need to reference the source code of either VMD
or NAMD for this task, however, you can find both freely available on the
site www.ks.uiuc.edu

Best of luck,

Rajan

On Fri, Jul 26, 2013 at 9:53 AM, Revthi Sanker
<revthi.sanker1990_at_gmail.com>wrote:

> Dear all,
> I am a novice to vmd and I am facing the same problem as in the thread:
>
> www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21277.html.
> As mentioned by Mr.Rajan, I would like to change the atom types to 3
> letter code. But kindly provide the information or link to the source code.
> I am unable to find it.
> Thank you for your help in advance.
>
>
> Revathi.S
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
> _________________________________
>