[gmx-users] x2top doesn't seem to recognize connectivity in the n2t file

[Arthur Roberts]

Hi, all,

I have been trying to convert a small molecule into
oplsaa format using the x2top.  The x2top doesn't seem
to recognize the connectivity specified in the n2t
file.

Below is the n2t file

; alkanes (first number is bond type and second number
is number of protons)
C	opls_138	4	H	H	H	H	; alkane CH4
C     opls_135	4	H	H	H	*	; alkane CH3
C     opls_136	4	H	H	C	*	; alkane CH2
C	opls_137	4	H	C	*	*	; alkane CH
C	opls_139	4	C	*	*	*	; alkane C
H	opls_140	1	C				; alkane H (sp3 hybridized proton)
; alkenes (first number is bond type and second number
is number of protons)
C	opls_141	3	C	C	C		; alkene R2-C=R
C	opls_142	3	H	C	C		; alkene RH-C=R
C	opls_143	3	H	H	C		; alkene H2-C=R
H	opls_144	1	C				; alkene H-C=	 (sp2 hybridized
proton)

I made a top file of an aliphatic and all the carbons
were treated as if they were the first one. i.e.
opls_138

Gromacs doesn't appear to recognize the connectivity
in ffgmx.n2t either.

I would appreciate anyone's input.

Best wishes,
Art