VMD-L Mailing List

From: Timm Essigke (essigke_at_chemie.fu-berlin.de)
Date: Fri Aug 04 2000 - 11:09:44 CDT

Hi,

I would like to draw some bonds between a metal ion and some sidechains
from a mol2 or a PDB file with CONECT records. The standard way to read
just a PDB and add the bonds by the distance criterion implemented in
VMD does not work because the distances are to large. There are some
non-standard residues, so it is a problem to put it into CHARMM to
generate a PSF. Is there a third way?
Can I add bonds over the command line (I found nothing in the manual)?
Is there a way to get VMD to read the CONECT records and use them
instead of its algorithm?
Is there any external program available which generates a PSF file form
such a PDB?

Any help is appreciated!

Thanks,

Timm 

-- 
Timm Essigke
Freie Universitaet Berlin * Fachbereich Biologie, Chemie, Pharmazie * 
Institut fuer Chemie (Kristallographie) * Takustr. 6 * D-14195 Berlin *
essigke_at_chemie.fu-berlin.de * http://www.chemie.fu-berlin.de/~essigke *
Tel.: +49-30-838-54627 * Fax.: +49-30-838-53464