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

From: Aseel Bala <>
Date: Tue, 21 Feb 2017 11:40:10 -0500

Thank you. This did it!

-----Original Message-----
From: Bill Ross []
Sent: Friday, February 17, 2017 1:54 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Creating a double bond in a pdb file with xleap

When one draws a structure in xleap, this is the one time that getting
double bonds right has any meaning in Amber: because the next step can be
Unit->Build (or Unit->add H and Build), which will cause the planar
structure to resolve into a reasonable 3D one, chemically speaking.

Clicking on bonds in draw mode to rotates bond order. Selecting and relaxing
as an alternative to getting bond orders right and using Build would be best
done after editing selected atoms and applying existing Amber types if


On 2/16/17 10:40 PM, Vaibhav Dixit wrote:
> 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.
> cheers.
> On Fri, Feb 17, 2017 at 3:20 AM, David Case <>
>> 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
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