Hi, I am building a frcmod file for a transition state of a
bimolecular reaction. The two molecules (one of which is OH-) are
separated by a 2.3 angstrom C10---O45 distance in the transition
state. In order to maintain this distance through simulation, I need
to add a bond for C---O. I wonder if there is a special bond type for
this situation. I also realized that in the mol.ac file generated by
antechamber (Amber 8.0) from the pdb file, the bond type is "9" for
the O45-H46 bond in OH- with a message "Bond types are assigned for
valence state 3 with penalty of 2". As I understand, "7" and "8" mean
the alternating single and double bond in benzene. What does "9" stand
for? Should it be a single bond "1"?
Thanks.
Eric
mol.ac
....
BOND 38 17 18 8 C17 C18
BOND 39 17 25 1 C17 H25
BOND 40 18 19 7 C18 C19
BOND 41 18 24 1 C18 H24
BOND 42 19 23 1 C19 H23
BOND 43 21 22 1 O21 C22
BOND 44 22 28 1 C22 H28
BOND 45 22 29 1 C22 H29
BOND 46 22 30 1 C22 H30
BOND 47 45 46 9 O45 H46
I add:
BOND 48 45 10 1 O45 C10
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Received on Wed Mar 02 2005 - 23:53:00 PST
