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

From: Aseel Bala <>
Date: Tue, 21 Feb 2017 11:40:21 -0500

Thanks for your help!

-----Original Message-----
From: Vaibhav Dixit []
Sent: Friday, February 17, 2017 1:40 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Creating a double bond in a pdb file with xleap

The attached file contains 3D coordinates for acetic acid and might help you.
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, SVKM's NMIMS, Mukesh Patel Technology Park Babulde, Bank of Tapi River, Mumbai-Agra Road, Shirpur, Dist. Dhule -425405 India.
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Received on Tue Feb 21 2017 - 09:00:03 PST
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