[gmx-users] query regarding a topology file

[Tsjerk Wassenaar]

Hi Jagannath,

I don't see why you have to "prepare a ff**bon.itp" to go with your
molecule.itp. In case the regular bond type definitions are not
sufficient, you can just add the bonds, angles, dihedrals directly in
the .itp file. The bond_types, angle_types and dihedral_types are
mainly used for proper handling of special bonds (as defined in
specbond.dat). Have a thorough read-through of Chapter 5 of the
Manual.

Best,

Tsjerk

On 4/13/07, Jagannath Mondal <jmondal at chem.wisc.edu> wrote:
> Thanks for reply. Yes, it uses the force-field file I created.
> Basically I found out that the dihedral which the program skips is
> also 0.
>
> On Apr 12, 2007, at 8:43 PM, Dallas B. Warren wrote:
>
> > Can't really help you directly, but it comes to mind when I read that
> > error that may be something is incorrectly defined or formatted within
> > your files.  It is not picking up the actual values, or something like
> > that?  Is it using the forcefield files you created?
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Lecturer
> > 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 9524
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to
> > resemble
> > a nail.
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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