VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jun 18 2012 - 04:11:03 CDT

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