ligands in VMD

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Wed Jun 01 2005 - 20:20:02 CDT

Hello

I have a lot of ligands without halogens, made of cycles with nitrogen
and carbon. I tried to read it into VMD with the tcl script

mol load pdb C8.pdb
#set sel [atomselect all]
#$sel writepdb ligand.pdb

package require psfgen
topology /home/RPMs/NAMD/toppar/top_alll27_prot_na.rtf
segment LIG {pdb ligand.pdb}
coordpdb ligand.pdb LIG
guesscoord
writepsf lig.psf
writepdb lig.pdb
exit

The C8.pdb have the following format

ATOM 5 C5 MOL d 1 4.620 -37.030 21.176 0.00 0.00
ATOM 6 C6 MOL d 1 5.739 -36.867 21.999 0.00 0.00
....
ATOM 17 C17 MOL d 1 -1.006 -36.157 20.631 0.00 0.00
ATOM 18 C18 MOL d 1 3.836 -39.059 17.261 0.00 0.00
....
ATOM 20 C20 MOL d 1 3.625 -40.285 16.614 0.00 0.00
ATOM 21 C21 MOL d 1 5.586 -38.542 15.668 0.00 0.00
 

so, atom names are meaningless. I really dont Know how Atom types are
generated for a structure like this. I thought topology files were
used to define from the atomic distances and the atomic enviroment
which atom type was better for certain atom. So which would be the
.pdb atom name format to allow VMD to generate a structure?? or I have
to define atom names a priori in the archive???

Please Help

Leonardo
Universidad de Chile

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