trevor brown wrote:
Dear friends,
I have the following topology for system including CNT+peptide+water
When I grompp for minimization, I got the following error. How can I
solve it?
best wishes
trevor
WARNING 1 [file ffbonded.itp, line 2703]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.14210 478900
You have a duplicate bondtype entry. Seems like you've got explicit C-C bonds
in one topology, and those parameters are replacing the default ones in
ffbonded.itp. Is that what you intend?
ERROR 1 [file ffbonded.itp, line 2709]:
Not enough parameters
In the ffbonded.itp provided in the Gromacs distribution, line 2709 is blank.
What have you added here?
-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: topio.c, line: 675
Fatal error:
Syntax error - File forcefield.itp, line 20
Last line read:
'1 3 yes 0.5 0.5'
Found a second defaults directive.
Something in your topology has gotten badly mangled. You can only ever have one
[defaults] directive that defines certain aspects of the force field.
http://www.gromacs.org/Documentation/Errors#Found_a_second_defaults_directive_file
TOPOLOGY
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
; Include topology for CNT
#include "cnt.itp"
; Include topology for UW1
#include "uw1.itp"
; Include water topology
#include "oplsaa.ff/spc.itp"
[ system ]
; Name
Protein and CNT in water
[ molecules ]
; Compound #mols
Protein 1
CNT 1
SOL 4019
In principle, this should work, if you've properly constructed the #included
.itp files, but I suspect something is wrong with one or more of them. Do any
of them re-#include "oplsaa.ff/forcefield.itp" (the peptide topology perhaps)?
-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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