[gmx-users] ffbond.itp

marzieh dehghan dehghanmarzieh at gmail.com
Mon Feb 23 07:04:06 CET 2015

Hi every body

1-      In the phosphate group, we have 4 oxygen atoms that bond to the
phosphate. Two of them are as follow: CH2-O-P-OH and the others include:

-          A double bond is on the top of phosphor atom

-          A OH group is at the bottom of phosphor atom

We put the atom type of OH group as OA, but We would like to know atom type
of each oxygen bounded to phosphate group. Because we cannot decide between
OA (hydroxyl, sugar or ester oxygen) and OM (carboxyl oxygen).

2-      If we can't find dihedral parameters of covalent bond for
ffbound.itp, please let us know, can we left blank it?
we are looking forward to getting your nice answer

thanks a lot

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

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