[gmx-users] improper doheldral to fix 6-member ring conformation

[Ester Chiessi]

Dear gromacs people,

I'm tring to build a correct topology to obtain a chair-conformation for 6-member
rings, with equatorial substituents in the 1-, 3-, 5- positions.
I looked at the beta-galactose and alpha-glucose residues topologies in but I
couldn't rationalize and I went on by trials and errors.

I noticed that I can variate the configuration of the quaternary carbon atom 'i',
by exchanging j and k atoms in the i j k l declaration. The improper angle is
between i,j,k and j,k,l planes. In what are different i,j,k,l, and i,k,j,l
impropers?

Thanks in advance for any explanation.

--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328