[gmx-users] amber and vsites

Erik Marklund erikm at xray.bmc.uu.se
Thu Oct 23 14:42:32 CEST 2008


I'm trying to get vsites working for my DNA decamer with ffamber03. I've 
added the following to ffamber03.ddb,

[ NH2 ]
; N2-CA in Adenosine/Guanine
amber99_38 planar

but pdb2gmx adds no virtual sites to the adenosines/guanines. What am I 
missing here?

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

More information about the gromacs.org_gmx-users mailing list