Where did you find the topology?
On Apr 10, 2012, at 10:44 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have doubt about definition of tiofen ring in MARTINI CG force
field. May I ask you to help me, Please?
I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-
C. Is it right?
Or should I change SC5 to C-S-C for .gro file?
And my definition of tiofen in .itp file it is as followed , Please
say me that is it right?
;;;;;; TIOFEN
[moleculetype]
; molname nrexcl
TIO 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC4 1 TIO SI1 1 0
2 SC5 1 TIO SI2 2 0
[constraints]
; i j funct length
1 2 1 0.27
Because I for benzene see a triangle in ngmx program, but for this
see a line. Please help me to correction of mistakes.
Thank you very much in advance.
Best Regards
Dina
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