VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jun 18 2012 - 17:05:56 CDT

I *think* paratool's (or maybe molefacture's?) topology file writer will also put an IC table in there; I know I did it once or twice before. It's rarely necessary though unless you're missing a lot of atoms.

On Jun 18, 2012, at 4:11 AM, Ajasja Ljubetič wrote:

> Dear all,
>
> After having successfully parametrized a new molecule, I would like to take care of one more convenience detail. Generating an internal coordinates table (so that building new residues is made easier).
>
> In charmm one would do something like:
>
> !Load the rtf and pdb
> GENErate MAIN SETUp ! generate segment with IC table
> IC FILL
> IC PRINT
>
> Here is an example output:
> ...
> ic n1p c1l c4 c5 1.5318 109.31 -70.29 118.76 1.5426
> ic c1o n1p c1l c4 1.5173 112.27 -113.59 109.31 1.5788
> ic c1n c1o n1p c1l 1.5689 100.39 3.33 112.27 1.5318
> ic o1m c1n c1o n1p 1.4041 108.28 -6.32 100.39 1.5173
> ...
>
> The problem is that I don't have acceess to CHARMM rigth now. So is there an easy way to generate the internal coordinates for use in CHARMM topology files using VMD?
>
> I have looked at the QMTool , Molfacture and the Paratools plugins, but there seems to be no easy way to print save or export the IC table in a suitable format.
>
> Thank you & best regards,
> Ajasja
>