The [ nonbond_params ] section is located in the nb.itp file of your chosen
force field. The error comes from the fact that you have likely tried to
introduce an additional [ nonbond_params ] directive within your .top file,
which is incorrect. You cannot have multiple entries for these directives, and
they must follow a certain order (given somewhere in the manual).
To introduce the additional atom type, you'll need to edit the nb.itp and .atp
file for your force field to account for the new atom type.
-Justin
Amir Marcovitz wrote:
Thank you Justin,
I didn't understand though where can I edit the [ nonbond params ] section?
Is there a better way to define pairs with no LJ attraction that will
ignore the settings in the *nb.itp file?
Cheers,
Amir
On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Amir Marcovitz wrote:
Hi,
my system is composed of two molecules, each is composed of a 36
carbon like dummy atoms i defined in the amber files (i.e., has
the LJ parameters of a carbon)
I'm interested in eliminating the attractive Lennard-Jones
interactions between the dummy atoms , such that only the
repulsive terms will account.
I thought of adding a section to the *.top file: [ nonbond
params ] and to set c6 to 0 such that the attractive term of the
LJ is eliminated.
I used exactly the same syntax of the tutorial (page 98):
* D D 1 0.00000E-00 0.34252E-05*
; (D is just the name of my dummy atom)
but got a syntax error when running grompp:
*Fatal error:
Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params*
1) what is wrong with my syntax? are there any further examples
anywhere for the usage of [ nonbond params ] in topology files?
If you have already #included a force field file in the .top, it
will have a [nonbond_params] section in it already. You cannot add
a new one. The proper approach would be to modify the #included
*nb.itp file.
2) Is [ nonbond params ] the right strategy to the task i described?
Sounds like one way to do it.
-Justin
Many Thanks,
Amir
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://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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