Peter C. Lai wrote:
[ angles ] is defined in ffbonded.itp. If you have new angles you will
need to specify them there. grompp will read ffbonded.itp and try to correlate
To be clear - [angles] can be specified in an .rtp file (but are not required,
because pdb2gmx will by default generate all angles). An [angletypes] directive
in ffbonded.itp supplies the parameters for angles.
it with the atomnumbers in the top file generated by pdb2gmx. If you modified
your top file by hand to include interactions which are missing from
ffbonded.itp then grompp will complain about missing interactions (at least
that is my experience).
Correct, but it is still not clear to me what the problem is here, if there is
one. The .rtp file would be necessary to understand what is expected in the
topology, as it is not clear to me why some lines have explicit parameters while
others do not.
-Justin
On 2012-03-07 05:19:19PM +0000, Lara Bunte wrote:
Hi Justin
I am using a CHARMM27 force field. I create a pdb file with the coordinates of
my molecule and I create a .rtp and a .hdb file for this. I also edit
atomtypes.atp, ffnonbonded.itp and residuetypes.dat
The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule.
The System is my molecule (isoalloxazine) in water.
Do you want to see my .rtp file?
Thanks you for helping me.
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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