VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Jun 18 2012 - 22:07:28 CDT

ParaTool can indeed do this. Load the PDB file in as the base molecule, then from Edit --> Internal coordinates select the "Autogenerate internal coordinates" button at the middle-center of the window. The box above will fill with the IC table. Then write out the topology file from File --> Write topology file.

I was unable to find a way to do the same thing in Molefacture.

Chris


On Jun 18, 2012, at 5:05 PM, JC Gumbart wrote:

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