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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