On 5/6/12 3:45 PM, Lara Bunte wrote:
Hi
You said:
The blank lines will be filled in with existing parameters from [angletypes] in
ffbonded.itp.
I let the lines empty and I got an error at the first grompp, before energy
minimization. grompp missed this empty lines. Here a part out of the errors:
ERROR 28 [file topol.top, line 229]:
No default Angle types
ERROR 29 [file topol.top, line 233]:
No default Improper Dih. types
My system is a cofactor, the force field is CHARMM27, parametrized with data
out of a supporting information of a group that determined this parameters for
my cofactor by experiments and quantum mechanical calculations. In
residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave
all informations (I guess).
What could be the problem?
I am able to complete the topol.top file by hand, but I really like to know
what is the problem here.
A sequence of atoms in a topology (defined by atom type, not name or number) is
mapped back to parameters in ffbonded.itp. If no suitable parameters are found,
you get the error messages. In a normal topology (.top or .itp) for most force
fields, the parameters are not explicitly stated because they are looked up in
this manner. If you're introducing something new or overriding existing force
field parameters, you need to explicitly include them in the topology or add
them to the appropriate directive in ffbonded.itp.
-Justin
Thanks for help
Greetings
Lara
----- Ursprüngliche Message -----
Von: Justin A. Lemkul<jalem...@vt.edu>
An: Discussion list for GROMACS users<gmx-users@gromacs.org>
CC:
Gesendet: 20:34 Dienstag, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote:
Hi
In some lines the equilibrium angle and the force constant is missing.I give
you an example:
The [ angles ] section is build like
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 19 1 123.75 250.00
1 2 3 1 123.75 250.00
1 2 4 1 117.47 230.00
And my pdb2gmx output is for example something like
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 19 1 123.75 250.00
1 2 3 1
1 2 4 1 117.47 230.00
So you have a complete topology and one that has missing parameters, or are you
adapting an incomplete topology?
What force field are you using? What is the system? For a normal protein system, most
force fields (all except Gromos, if I recall) produce bonded directives with no
parameters; they are looked up from ffbonded.itp and not stated explicitly, so
"missing" parameters are completely normal and not problematic. If you're
dealing with something nonstandard and you've had to create .rtp entries, you'll need to
post that information for diagnostic purposes.
In principle, there's nothing wrong with any of this. The blank lines will be
filled in with existing parameters from [angletypes] in ffbonded.itp. These
parameters are only overwritten if explicitly present in the topology. If
there is a bonded interaction referenced in the topology that does not exist in
ffbonded.itp, grompp will fail with a fatal error.
-Justin
-- ========================================
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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--
========================================
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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