AMBER Archive (2009)

Subject: RE: [AMBER] antechamber cation failure

From: Ross Walker (
Date: Wed Jan 14 2009 - 11:45:43 CST

Hi Rausch,

> I try to set up some QM/MM calculations for a protein using AMBER10.
> Therefore, I have to prepare the ligand (terpinyl cation) with
> antechamber.

Technically if you will be treating the ligand with QM you do not need to
set it up in antechamber you just need to build it in a way that allows you
to generate a prmtop file. You could just load this into leap and draw in
the bonds yourself (not strictly needed but helpful) - set some random atom
types, set all the charges to zero etc.

> I tried to do so by using the following command:
> antechamber -i TCA.pdb -fi pdb -o TCA.prepin -fo prepi -c gas -s 2 -nc 1

Your attached TCA.pdb file seems to have some strange characters in it. If I
open it in VI I see a whole column after TCA with the control character ^@
in it. This confuses VMD and may confuse parts of antechamber as well. If I
repeat what you did with the corrupt pdb file I get the same error. However,
if I remove the ^@ column and replace it with a space then I can view it in
VMD but antechamber still quits with the same error.

However, looking at this further I see several possible problems.

The first is that you are asking for Gasteiger charges (-c gas) which
shouldn't make any difference if you are running the ligand QM since they
will be ignored however just in case you probably want to use AM1-BCC here
so set this to -c bcc.

The real problem though is that this is somewhat of a strange structure for
an organic compound. Note the trivalent carbon with the two methyl groups
hanging off it. I suspect that antechamber does not know how to deal with
this. Is this indeed a +1 charged organic ligand with a trivalent carbon? If
so then you may need to include the counter ion in the antechamber
calculation - alternatively you may just have to manually build this
yourself in leap - see for
an example that you should be able to use as a basis for building this with
dummy parameters (note the mass and VDW params should be correct for the
atom types, as should the eqm distance for bonds to hydrogen if you plan to
use shake in the QM region.)

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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