[gmx-users] Planar group (again)

David spoel at xray.bmc.uu.se
Sat Mar 27 10:12:01 CET 2004

On Fri, 2004-03-26 at 23:34, Coincon Mathieu wrote:
> I am sorry if my questions seem to be always the same but I have again
> difficulty to keep a group of atom planar after minimisation (the
> first time I succed). 
> You could find a description of my molecule on this site with my  
> .itp file. 
> http://www.ESI.UMontreal.CA/~p0661390/gromacs_planar.htm
> What g_di (I use ffG43a1) or what exclusions I have to add to keep my
> atoms planar ? 
> I already treid to exclude my oxygens and/or my HH. 
> My charges are an "average" of charges given by gaussian and charges
> taken fron different groups of the .rtp library. Could it be a problem
> here ? 
No, although you will have to justify this at some stage (i.e. for a

You need to add impropers
C7 C10 C11 OC1
C9 C10 C11 H11

and some more in the rings. For pure benzene you need six impropers
around the ring and six to keep the hydrogens in the plane. You are
still missing some of these it seems. On the other hand you have
duplicated at least one (the first)...

> -- 
> Mathieu Coincon PhD Student
> Universite De Montreal/Departement de biochimie 
> Pavillon Roger Gaudry Local D345
> (514).343.6111 #5352
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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