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.
-Justin
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, <[email protected]> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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