VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Nov 06 2008 - 12:04:06 CST

Hi Vaithee,
did the warning come from molefacture or from psfgen? Molefacture should
issue a warning to this effect whenever you have more than one atom of
the same type and you ask it to generate a topology file. As long as all
of your atoms typed CA really are equivalent, everything is fine -- the
warning is only present to make sure that people really mean their types.
Best,
Peter

Subramanian Vaitheeswaran wrote:
> 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
>