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 Mon Feb 18 2013 - 11:00:03 PST
