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

[Arthur Roberts]

Thanks, David.  I will try it out and tell you how the
results went.

Best wishes,
Art

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 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
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>