[gmx-users] Ryckeart Bellemans parameters for Fe coupled to cystines

saurabh shakya shakya_79 at yahoo.com
Mon Dec 15 13:29:01 CET 2003

Thanks for the suggestion Dr Warren. I tried what you
suggested ,ie, removing the 1-4 interaction pairs for
the troubling hydrogens but even this doesn't seem to
work and i get the lincs error again for the same
hydrogens ..does it has to do something with the RB
dihedrals ? Currently I have specified the dihedrals
for these hydrogens as proper .

With best regards
Saurabh Kumar Shakya.
>this additional Fe .  Specifying the dihedral as a
>proper dihedral (type 1) always leads to links error
>with the hydrogens of cystines rotating more than 30
>degrees. Can I specify dihedral as proper(type 1) in
>place of RB type (type 3).

In some cases this can be due to interactions between
the hydrogen and 
another atom in the 4 position.  The interactions are
too strong for what 
they actually should be, hence the LINCS error that
you get.  Somewhere (I 
think in the manual or may be somewhere else) it
mentions that you can 
remove the 1-4 interactions (pairs) to stop that

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083

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