[AMBER] Topology issue with MMPBSA.py

From: JPB <jpb.q4md-forcefieldtools.org>
Date: Mon, 16 Jun 2014 12:29:39 +0200

Dear All,

I am getting use to running MMPBSA.py 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?

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 MMPBSA.py 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.

The MMPBSA input file is:

    startframe=10, endframe=100, interval=10,
    verbose=2, keep_files=1, netcdf=1,
    nmstartframe=1, nmendframe=100, nminterval=1,

All the other input/output files as well as the topologies and trajectory
are accessible with this link:

contains the topology of vinylbenzene solvated with TIP3P waters.

contains the "dry" topology of vinylbenzene.

is the directory where the short MD of vinylbenzene was run.

is the directory where the mmpbsa job was run.

With anticipated thanks.

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Received on Mon Jun 16 2014 - 04:00:02 PDT
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