[gmx-users] ffbond.itp

marzieh dehghan dehghanmarzieh at gmail.com
Tue Feb 17 13:27:45 CET 2015

Hi every body
*in order to complete ffbond.itp for new covalent bond, we use the
following article A Biomolecular Force Field Based on the Free Enthalpy of
Hydration and Solvation: The GROMOS Force-Field **Parameter Sets 53A5 and
53A6",but we can't find out how to solve these problems?*
*1-Gromos angle (ga_????) for "CH1-C-CH2"?*
*2-How to determine "atom type" for oxygen bonded to phosphate group?*
*3-Dihedrals parameters for the following cases:*
*C CH1 O CH2*
*CH1 CH2 OA P *
*CH2 CH1 OA H*
*CH1 CH1 CH1 CH2*
*C CH1 CH1 CH1*

*CH1 CH1 C CH2*
thanks a lot

best wishes

*-- *

*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*

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