[gmx-users] methane??

[David]

On Fri, 2003-07-11 at 03:30, Vivek Raut wrote:
> I have methane molecule (Ch4) as one of the atoms of the systems. But 
> GROMACS does not accept that molecule while making a .gro file from .pdb 
> file. I looked in atom types & it doesnt define a carbon with 4 hydrogens 
> attached to it,
> 
> How does /can GROMACS read methane then?
you have to make the topology manually (or using prodrg). chapter 5 in
the manual. the only pitfall is that when using constraints you should
leave out one of the ten possible otherwise you will have only 5 degrees
of freedom left (out of 6).
> 
> -------------------------------------------------------------------------------------------------------------------------------------------
> Vivek Raut
> Graduate Research Assistant
> Department of Bioengineering
> Clemson University
> Clemson, SC- 29631. USA
> Email: vraut at clemson.edu
> Phone: 864-650-1431
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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