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

[David van der Spoel]

Arthur Roberts wrote:
> 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 
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I presume this is in 3.3.1?

try installing the CVS branch in a separate tree and run x2top from 
there. There have been a number of improvements in that program.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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