AMBER Archive (2009)

Subject: [AMBER] formate parameters

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Tue Feb 10 2009 - 08:47:31 CST

Hello, I`m interested in formate molecule (HCOO-) parameters for my
simulation,
so I try to use Antechamber and Parmchk programs:
"antechamber -i formate.pdb -fi pdb -o formate.mol2 -fo mol2 -c bcc -s 2 -nc
-1"
and then "parmchk -i formate.mol2 -f mol2 -o formate.frcmod".

So, obtained formate.mol2 file is
..........
@<TRIPOS>ATOM
      1 C 10.4500 2.9000 16.9600 c 1 FMT 0.904300
      2 O1 9.9040 1.8030 16.9300 o 1 FMT -0.877800
      3 O2 10.1390 3.9420 17.5520 o 1 FMT -0.878000
      4 H 11.2860 2.9650 16.4150 h5 1 FMT -0.148400
@<TRIPOS>BOND
     1 1 2 1
     2 1 3 1
     3 1 4 1
...........

and obtained formate.frcmod file is
...........
BOND
c -h5 357.50 1.078 same as c2-h5
ANGLE
o -c -h5 55.400 120.000 same as hc-c -o
DIHE
IMPROPER
h5-o -c -o 1.1 180.0 2.0 General improper
torsional angle (1 general atom type)
............

I'm confused with proposed angle "o -c -h5 55.400 120.000 same as
hc-c -o".
This is description of atom types in $AMBERHOME/dat/leap/parm/gaff.dat:

c Sp2 C carbonyl group
o Oxygen with one connected atom
h5 H bonded to non-sp3 carbon with 2 electrwd. group
hc H bonded to aliphatic carbon without electrwd. group

So I`m confused with substitution of h5 to hc because oxygen in carbonyl is
electron withdrew
(It conflicts with hc definition).
Could you explain what chemical compound does angle hc-c -o correspond to in
general?
And is proposed angle "o -c -h5 55.400 120.000 same as hc-c -o"
appropriate to formate molecule?

Thank you!

Dmitri Nilov,
Lomonosov Moscow State University
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