On 2013-02-18 10:16, Cuong Nguyen wrote:
Dear Gmx-users,
I have ions.itp file for polarized Na+ and Cl- as follows:
; Sodium, Na+
[ moleculetype ]
; molname nrexcl
Na+ 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 Nac 1 Na+ Nac1 1 +0.312403
2 Nas 1 Na+ Nas1 1 +0.687597
[ polarization ]
; See notes above. alpha (nm^3)
1 2 1 0.00024
[ exclusions ]
; iatom excluded from interaction with i
1 2
2 1
; Chloride, Cl-
[ moleculetype ]
; molname nrexcl
Cl- 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 CLc 1 Cl- CLc1 1 -4.457187
2 CLs 1 Cl- CLs1 1 +3.457187
[ polarization ]
; See notes above. alpha (nm^3)
1 2 1 0.00325
[ exclusions ]
; iatom excluded from interaction with i
1 2
2 1
and after running the command:
*grompp -f ions.mdp -o min.tpr -c box1.g96*
it appears the error:
Program grompp, VERSION 4.5.5
Source code file: topio.c, line: 656
Fatal error:
Syntax error - File ions.itp, line 20
Last line read:
'[ exclusions ]'
Invalid order for directive exclusions
Please help me to deal with this issue?
remove the exclusions. Since there are no bonds you can not have
exclusions. Exclusions will nevertheless be generated. Please check the
topology using gmxdump.
Thanks a lot in advance.
Best regards,
Cuong
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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