[gmx-users] pdb2gmx - .top missing values

[Dallas Warren]

>Therefore it gets correct where all the bonds are, angles etc.  However, 
>it has left out the details of how long they are, force constants etc.  As 
>I said in the previous email, I assumed that these would all be inserted 
>into the .top file to then be subsequently used by the rest of the 
>software.  If this isn't the case, then I don't actually have a problem at 
>all then, was just expecting something else.

Well, I got to the stage today (having sorted out the force field, residues 
etc) to start to use the .top file generated by pdb2gmx using the new 
residues I had defined.  However, grompp comes up with a warning that there 
are no default angles suppled in .top, and has to use zeros.  That comes up 
10 times then it halts, since 10 warnings is where it is meant to.

Therefore, from this I assume that pdb2gmx should be putting the bond 
details, not just which atoms are involved, into the .top file.

Are there any suggestions on why it may be the case that it isn't putting 
those into the .top?

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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