VMD-L Mailing List

From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Thu Nov 06 2008 - 11:25:01 CST

Hi all,

I am using the following script to generate a set of psf and pdb files:
******************
package require psfgen
topology Tube1.top
segment T1 {
           pdb new_tube.pdb
           first none
           last none}
coordpdb new_tube.pdb T1
regenerate angles dihedrals
writepdb tube_dih.pdb
writepsf tube_dih.psf
******************
The first few lines of Tube1.top are:
******************
*>>>>>> CHARMM topology file generated by Molefacture <<<<<<
27 1
                                                                                
MASS 1 CA 12.01100 C
                                                                                
AUTO ANGLES DIHE
                                                                                
RESI CNT 0.00
GROUP
ATOM C1 CA 0.00
ATOM C2 CA 0.00
ATOM C3 CA 0.00
  . . .
******************

The output pdb and psf files seem to be fine, but I get a warning on running the script: "Warning: Multiple incompatible definitions of type CA. Using the first". No other topology file is called - can anybody explain what's causing this? I assume it is safe to ignore, since the output files are fine. Any thoughts on this?

Thanks in advance,
Vaithee