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

From: Bill Ross <>
Date: Thu, 16 Feb 2017 22:54:10 -0800

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 possible.


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 <> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Feb 16 2017 - 23:00:02 PST
Custom Search