Re: [AMBER] Topology issue with

From: JPB <>
Date: Mon, 16 Jun 2014 15:37:06 +0200

Hi Jason,

Thanks for quick answer and insight.

To clarify the warning message itself:
C: 11 1;
means the C atom number 11 has only 1 bond, doesn't-it?
I was not clear where the 1 was coming from.

I had already checked my topology with xleap and vmd
and this is one of the reasons this message was so disturbing.

Moreover, all the other carbon atoms in the structure are described
by CA type as well, each of them have 3 bonds, and none of them causes
I also tried a similar computation with the same procedure on
ethylbenzene and everything went smoothly, no warning message.
It really looks like an Sp2 (in vinylbenzene) carbon at this
particular position
triggers the output of the warning message and not a Sp3 one (in
As I said, it is still kind of disturbing.


Jason Swails <> a écrit :

> On Mon, 2014-06-16 at 12:29 +0200, JPB wrote:
>> Dear All,
>> I am getting use to running jobs.
>> For this purpose I am working on vinylbenzene.
>> In the _MMPBSA_complex_gb.mdout files the following error message appears:
>> bad number of bonds to C: 11 1; using default carbon parameters
>> I did not manage to solve this problem.
>> Another thing which is a little confusing is the numbering of atoms in this
>> error message.
>> In the _MMPBSA_complex.pdb file, atom number 11 is hydrogen, not carbon.
>> After several attempts on different systems and with different atom
>> orderings, it seems that the atom numbering starts from 0 in the error
>> message and not from 1 like in the pdb file.
>> Is this correct? Can anybody confirm it?
> Yes, this is correct. This message is printed by NAB (a C-based
> language), in which arrays are indexed from 0 instead of 1 (as in
> Fortran-based programs like sander and pmemd).
>> Here is the procedure followed for this computation:
>> 1. generation of a topology for solvated vinylbenzene with tleap.
>> 2. generation of a topology for vinyl with tleap (dry topology).
>> 3. running a short molecular dynamics of vinylbenzene with pmemd in
>> TIP3P water
>> using the solvated topology.
>> 4. rewriting the trajectory removing water molecules with cpptraj.
>> 5. running on the trajectory without waters using the dry
>> topology.
>> It seems the carbon atom making trouble is the one at the end of the
>> vinyl group to which two hydrogen atoms are linked.
>> (cross-checked on other compounds)
>> Any help to solve this issue would be deeply appreciated.
> can actually automate step 4 for you, in case you cared.
> In any case, this seems like a warning, not an error, but it is a
> concerning warning. Atom number 12 here is recognized as a carbon atom,
> but only 1 bond to that atom is detected. Carbon forms at least 2 bonds
> (think alkyne or allene) in any biologically relevant system. So if one
> of your carbon atoms has only a single bond you need to find out why and
> fix it.
> However, this error is printed out by the LCPO calculation in
> mmpbsa_py_energy, which is actually ignored entirely by in
> AmberTools 12 or 14. The SASA calculation is dispatched to cpptraj
> (which determines the element based on the atomic number rather than
> based on the atom type name). So if you are confident that there is no
> such error in your system, you can safely ignore this warning.
> As a hint, visualizing your system (using your prmtop in VMD, _not_ by
> converting to a PDB first) can help you detect missing bonds or other
> oddities in your topology.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

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Received on Mon Jun 16 2014 - 07:00:03 PDT
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