Dear Jason,
Thank you for your comment. If I may, I'd ask one more question regarding
your comment. You mentioned that I can ignore the bond types for the
topology file. Does this mean that all the force field parameters will be
correctly assigned and written in the topology file even without correct
bond-type information ? (assuming that the atom types are correct).
Thank you in advance for your help.
Best,
Charles
On Mon, Feb 18, 2013 at 1:51 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Feb 18, 2013 at 1:44 PM, Charles Do <cdonssim.gmail.com> wrote:
>
> > Hi all,
> >
> > In the past few days, I've been trying to create a molecule with a few
> > residues. For each residue, I was successfully able to run antechamber to
> > get bond-types and atom types correctly. Some of the bonds involve
> aromatic
> > bond and double bonds. (ar or 2).
> >
> > Within the xleap. I loaded these residues and created a new molecule by
> > using sequence command. The resulting structure was successful and looked
> > ok. However, once I save the structure using 'savemol2' all the
> bond-type
> > information was gone and all the bond types were set to '1' (single
> bond).
> >
> > How can I preserve the bond types of the consisting residues and
> > successfully save it as mol2 file?
> >
>
> I do not think you can do this using tleap since tleap doesn't know what a
> `bond order' is. If you only want to use the mol2 file to generate a
> topology file, then ignore this. Otherwise, you can either hand-edit the
> bond orders or use a program that respects them to generate your mol2.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Feb 19 2013 - 07:00:03 PST
