[gmx-users] query regarding a topology file
tsjerkw at gmail.com
Fri Apr 13 21:37:26 CEST 2007
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
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.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
More information about the gromacs.org_gmx-users