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

From: Aseel Bala <>
Date: Thu, 16 Feb 2017 15:47:27 -0500

Thank you for your response.
I didn't create these coordinates manually. Xleap created them when I
relaxed the structure.
To generate this file I did the following:

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.

 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

Do you have any suggestions on how to correct this issue?


-----Original Message-----
From: David Case []
Sent: Wednesday, February 15, 2017 9:31 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Creating a double bond in a pdb file with xleap

On Wed, Feb 15, 2017, Aseel Bala wrote:
> I am trying to create an acetic acid molecule with xleap and generate
> a pdb and mol2 file. I am able to create the molecule in xleap.
> However, I am not able to add the double bond between the C and O.

The error you see has nothing to do with creating or not creating a double
bond. In fact, PDB files have no notion of bonds or bond orders, and
antechamber doesn't expect to find any such information in the PDB file.

Rather, your problem is that the z-coordinates of all atoms are zero: you
have a planar molecule(!), whereas antechamnber expects (and requires) a
reasonable input configuration.

       ATOM 1 C1 aaa 1 12.735 -2.914 0.000 1.00 0.00
> ATOM 2 C2 aaa 1 11.238 -3.020 0.000 1.00 0.00
> ATOM 3 H4 aaa 1 12.805 -3.912 0.000 1.00 0.00
> ATOM 4 H5 aaa 1 13.590 -3.432 0.000 1.00 0.00
> ATOM 5 H6 aaa 1 13.253 -2.059 0.000 1.00 0.00
> ATOM 6 O7 aaa 1 11.776 -4.420 0.000 1.00 0.00
> ATOM 7 O8 aaa 1 10.057 -3.945 0.000 1.00 0.00
> ATOM 8 H9 aaa 1 9.213 -3.408 0.000 1.00 0.00

It's not clear how you created these coordinates, but if you view your pdb
file in a molecular viewer, you will immediately see the problem. You need
to create a good geometry: in xleap, consider selecting all atoms and
choosing the "relax selection" option in the menu.

...good luck....dac

AMBER mailing list

AMBER mailing list
Received on Thu Feb 16 2017 - 13:00:03 PST
Custom Search