Re: [AMBER] Topology issue with

From: Jason Swails <>
Date: Mon, 16 Jun 2014 08:27:52 -0400

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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 16 2014 - 05:30:02 PDT
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