[gmx-users] pdb2gmx - .top missing values

[Dallas Warren]

>Yes -- that is what grompp does, at least its mayor task.
>It reads in all the [*_types] definitions from the *.top and *.itp
>files specified, and uses those to fill in all the blanks in the
>[bonds] [angles] etc. definitions. If you prefer, you could also

FYI, I have now sorted this all out.

I checked the bond/angle/dihedral warnings that grompp came up with against 
what was in the force field.  Surprise, surprise, they weren't there.  Once 
I defined them, things work fine.

On another note, a suggestion for who ever puts together the manual etc.  A 
short summary of the type of information that can be obtained from all the 
analysis scripts provided with the software package might be an idea.  Each 
time I read through the chapter that outlines how to use them I discover 
something new.  And some of them are a little cryptic.

To those that have developed GROMACS, well done.  The more I use it, the 
more I see how powerful, yet flexible, it is.  Takes a bit to get into 
though ;-)

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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