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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