AMBER Archive (2009)

Subject: [AMBER] Input file of the second stage RESP fitting

From: Cen Gao (
Date: Mon Mar 16 2009 - 23:29:17 CDT

Dear Amber Users:

Sorry to trouble, I have several questions regarding the input file of
the second stage RESP fitting. Any input is highly appreciated.

1. How does the ivary variable assigned for each atom in the input
file of second stage RESP? (this value was suggested to set to 0 in
the first stage) R.E.D. tool seems to assign it depending on the P2N
file made by On the other hand, respgen in $AMBERHOME/bin
can also automatically generate input from an .ac file. I was
wondering if I should preferably use one over the other? We already
have the electric potential generated on a grid so we only need the
input file to do resp. Can I easily get the input without running the
QM calculations if R.E.D is used? (We only do single conformation
charge fitting)

2. I suppose "-1" and "-99" means the same in the ivary section,
right? (charge frozen at initial charge?)

3. What does the "-99 29" mean in line 7 of the file at
$AMBERHOME/examples/resp_charge_fit/bis-napthyl/ From the
manual, this line refers to "charge, iuniq"? I don't get the charge
part. -99 certainly cannot be the net charge of that molecule. Does
the "-99" mean the same as the one in ivary, which indicates "charge
frozen at initial charge"? But there is no initial charge file
available (-q option was not supplied in this stage).

Again, thanks for helping me out on this.



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