From: Axel Kohlmeyer (
Date: Sun Aug 05 2007 - 12:35:15 CDT

On Sun, 5 Aug 2007, Francesco Pietra wrote:

dear francesco,

FP> Hi Peter and Axel:
FP> The file format I use for Amber can be fully grasped from

actually, the amber file formats are documented at:

as you can see, there is no element information, but
one could do some educated guess based on the atom
masses (with the problems outlined before). in the
long run, VMD should get a generic 'guess the element'-function
that is used by all plugins, where the file format
does not provide explicit information.

FP> the last section is for solvents I used *** and frcmod.**** Although I
FP> used such files directly from Amber9, they should be the same format.

well, you don't read those files into VMD, but the topology in
parm7 format, so that format is what matters. please always
remember VMD has no knowledge of chemistry (or physics) and
particularly - as all computer software - no common sense.

FP> As to coloring by element, selection of "element" in "Graphical
FP> Representation" of VMD only returns "X". To give an idea, if I command

yep. that confirms, that the amber topology plugin does not
try to guess the elements from the masses.

you can either set the element information yourself with some
VMD scripting based on a list of the atom type to element mappings
for your specific case, or just adjust the colors in the Name or
Type coloring style to your liking.


FP> all not element X
FP> everything disappears from the screen.
FP> francesco

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.