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

From: David Case <>
Date: Thu, 16 Feb 2017 16:50:32 -0500

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.


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Received on Thu Feb 16 2017 - 14:00:03 PST
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