RE: AMBER: Leap adding extra atoms

From: Scott Brozell <>
Date: Mon, 15 Jan 2007 12:39:49 -0800


On Thu, 11 Jan 2007, Akshay Patny wrote:
On Thu, 11 Jan 2007, Bill Ross wrote:
On Thu, 11 Jan 2007, Akshay Patny wrote:

> > > I have ran antechamber on telmi.pdb using RESP method
> > > (the ligand contains a formal charge of -1).
> > > I have got the following files Telmisartan_charged_frcmod and
> > > Telmisartan_charged_resp.prep

> > > Loading PDB file: ./telmi_mod.pdb
> > > Created a new atom named: N5 within residue: .R<TEL 298> <<<==== e.g. N5
> > > Created a new atom named: C35 within residue: .R<TEL 298>
> > > Created a new atom named: O3 within residue: .R<TEL 298>
> > > Added missing heavy atom: .R<TEL 298>.A<O2 60>
> > > Added missing heavy atom: .R<TEL 298>.A<N4 42> <<<==== e.g. N4
> > > Added missing heavy atom: .R<TEL 298>.A<C33 25>
> > > total atoms in file: 39
> > > Leap added 32 missing atoms according to residue templates:
> > > 3 Heavy
> > > 29 H / lone pairs
> > > The file contained 3 atoms not in residue templates
> > >
> >
> > Notice the atom names. The names in your pdb must match the ones
> > in your template. Leap cannot determine that e.g. N4 in the
> > template is the same and N5 in your pdb.

> I understand that now. However, I generated the PREP file for my ligand e.g.
> DMPC monomer from the input MOL2 ligand file attached. Now, the template
> PREP file which is generated has all of atom names different from that of
> the input MOL2 file names.

Exactly what has been done is not clear. For example
DMPC_mono_sybyl.mol2 contains only 1 nitrogen atom
Telmisartan_charged_resp.prep contains 4 nitrogen atoms
telmi.pdb contains 4 nitrogen atoms
telmi_amber.pdb contains 5 nitrogen atoms

> 1. Is this change of atom names during PREP file generation occurred because
> I used input as MOL2 file?

antechamber should have an option to prevent atom name changes, but
it does not.

As I recall, antechamber serializes all atom names when creating prep
files; and the input format is immaterial.
For example, telmi.pdb has N2, N1, N, and N3 atom names;
Telmisartan_charged_resp.prep has N3, N2, N1, and N4 atom names.
(If you use prepc format then you can verify which was which by comparing
the Cartesian coordinates.)
For example, DMPC_mono_resp.prep has C1, ..., C36.
DMPC_mono_sybyl.mol2 has CN1, ..., CA, C2A, C2B, ...
(in other words names that are completely unconventional relative to proteins).

> 2. Should I have used PDB as the input file, does using PDB as input file
> keep the same atom names in the template PREP file?
> 3. As for using RESP, I have to use gaussian, the atom name information is
> lost during the gaussian job, so should it matter whether to use input file
> as MOL2 or PDB??

One way to avoid problems is to use antechamber to create all files
(including initial pdb and gaussian input files).

But antechamber should have an option to prevent atom name changes.

> In any case, my template PREP file which is generated has all of atom names
> different from that of the input MOL2 file names, how can I take care of
> that now??

The simplest approach is to redo what you have done starting from
fresh input files that have already been made antechamber safe.
(I think I have done this via a pdb to pdb antechamber run or maybe
I had to do pdb to prepc to pdb. Sorry extraneous issues prevent me
from tracking this down today.)

Alternatively, you could transform the names of atoms in
your files so that they are consistent,
maybe with the help of the prepc format; but this could be
a dangerous approach, attention to detail is critical.

If there are a small number of atom name changes then simply recording
the mappings in your lab notebook and applying them manually may be


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Received on Wed Jan 17 2007 - 06:07:56 PST
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