Re: [AMBER] Creating a double bond in a pdb file with xleap

From: Vaibhav Dixit <>
Date: Fri, 17 Feb 2017 12:10:03 +0530

The attached file contains 3D coordinates for acetic acid and might help
I have drawn them using Marvinsketch and generated conformations using
default options.

On Fri, Feb 17, 2017 at 3:20 AM, David Case <> wrote:

> On Thu, Feb 16, 2017, Aseel Bala wrote:
> >
> > I opened xleap and drew an acetic acid molecule except (because I
> couldn't
> > figure out how to add a double bond), I just had a single bond between
> the C
> > and O where there should really be a double bond. Then I relaxed the
> > structure and saved the result as a pdb file.
> Did the structure look correct (in xleap) before you saved to a PDB file?
> >
> > I was hoping that I could just generate a pdb and mol2 file in xleap and
> > then manually modify the bond order in the mol2 file for the bond
> between C
> > and O. However, xleap cannot generate a mol2 file because the number of
> > atoms and bonds do not make sense unless there is a double bond between
> the
> > C and O. And I think this is also the reason that it zeroed out the
> > z-coordinate.
> I don't agree: the methyl part of your molecule is completely planar, and
> that has nothing to do with single or double bonds. Your result is
> entirely
> compatible with the following scenario: you drew the molecule as a plane
> (which is xleap's default.) Then, either you didn't really relax it, or
> the relaxation failed because starting from a completely planar structure
> is
> pathological, and the system doesn't know how to break the planar symmetry.
> Play around with how you draw the structuer in xleap (say choose just the
> methyl group, and relax that; then relax the rest). Maybe other procedures
> will be required: e.g. edit the ASP residue to remove the parts you don't
> want
> to get back to acetic acid.
> Bottom line: you need to get a good geometry, and I don't think this has
> anything to do with the assignment of single or double bonds.
> ....dac
> _______________________________________________
> AMBER mailing list

With Regards.
Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
IISc, Bangalore)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
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Received on Thu Feb 16 2017 - 23:00:02 PST
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