[gmx-users] grompp fatal error Unknown bond_atomtype

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 23 23:46:41 CEST 2010

Are you using the most recent git version?  I think the date string indicates 
you're using a version that's several months old (I could be wrong).  If you 
haven't pulled the latest git, please do.  There have been several changes 
related the the CHARMM implementation and bugs that have been discovered.


Peter Huwe wrote:
> Thanks for the response, Chris.  And sorry that I was not detailed
> enough earlier.  I've read through the manual several times, and I'm
> familiar with all of the passages that you cited.  I am parameterizing
> PtdIns4,5P2.  OSL is one of the atom types in it (it is a phosphate
> ester oxygen).
> OSL is in my atomtypes.atp file.
> OSL is also in my .rtp file.  I have 6 OSL type atoms (named O1, O13,
> OS1, OI1, O4P, & O5P), and each seems to be paired correctly in
> accordance the rtp. format.
> My problem is that I do not know the origin of the "Fatal error:
> Unknown bond_atomtype OSL" error that grompp gave me.  Obviously there
> is a problem with one of my files, but which one?  The .atp, the .rtp,
> the bon.itp???  I've never received this particular error before. Any
> guidance is appreciated.
> Thanks,
> Peter
> On Tue, Jun 22, 2010 at 11:00 PM,  <chris.neale at utoronto.ca> wrote:
>> There's lots of information in the gromacs manual to show that the .atp file
>> is not the only file that you must modify. My most important suggestion to
>> you is that you should read the entire manual, possibly twice, before
>> attempting to build new molecules.
>> Gromacs manual, page 96:
>> 5.3.1    Atoms
>> A number of static properties are assigned to the atom types in the GROMACS
>> force field: Type, Mass, Charge, and ? (see Table 5.2 The mass is listed in
>> ff???.atp (see 5.2.1), whereas the charge is listed in ff???.rtp (.rtp =
>> residue topology parameter file, see 5.6.1). This implies that the charges
>> are only defined in the building blocks of amino acids or user defined
>> building blocks. When generating a topology (*.top) using the pdb2gmx
>> program the information from these files is combined.
>> Then on page 97:
>> "In the file ff???bon.itp you can add bonded parameters. If you want to
>> include parameters for new atom types, make sure you define this new atom
>> type in ff???.atp as well."
>> Then on page 120:
>> For each force field there a five files which are only used by pdb2gmx.
>> These are: the residue database (.rtp, see 5.6.1) the hydrogen database
>> (.hdb, see 5.6.2), two termini databases (.tdb, see 5.6.3) and the atom type
>> database (.atp) which contains only the masses.
>> I'm not going to post a detailed account of how to add an atom because it is
>> key for you to fully understand what all of the forcefield files are doing
>> if you are going to do something like create a new atom type. The
>> information is all in the manual though, and search "exotic species" on the
>> wiki, although lots of links there are still broken after the migration to a
>> new wiki type.
>> By the way, you didn't post nearly enough information! You are trying to
>> parameterize a new molecule and you got an error and the only thing that you
>> posted was the error message ..... you're much more likely to get good help
>> if you make it easier for everybody else to help you.
>> Chris
>> -- original message --
>> Hi Users,
>> I am experiencing the following fatal error when I try using the
>> grompp command.
>> grompp -f mdout.mdp -r conf.gro -p topol.top
>> .
>> .
>> .
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.99-dev-20100409-0045555
>> Source code file: toppush.c, line: 631
>> Fatal error:
>> Unknown bond_atomtype OSL
>> .
>> .
>> .
>> OSL is defined in the atomtypes.atp file located in the force field
>> folder that I constructed.  Thus, I do not understand why it is
>> "unknown."
>> Does anybody know how to address this error?
>> Many Thanks,
>> Peter Huwe
>> --
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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