Dear AMBER users,
I did a RESP fit on guanine (RG), capped with a methyl
group at N9. I knew I wouldn't get the same charges as
those in all_nuc94.in, but I wasn't expecting such big
differences:
atom all_nuc94.in my charges
----------------------------------
N9 0.0492 -0.008536
C8 0.1374 0.119023
H8 0.1640 0.152369
N7 -0.5709 -0.529202
C5 0.1744 -0.031449
C6 0.4770 0.737717
O6 -0.5597 -0.586775
N1 -0.4787 -0.819068
H1 0.3424 0.416906
C2 0.7657 1.041551
N2 -0.9672 -1.120108
H21 0.4364 0.468264
H22 0.4364 0.468264
N3 -0.6323 -0.771436
C4 0.1222 0.358782
----------------------------------
total -0.1037 -0.1037
The total charge on the methyl group was constrained
at 0.1037, which made the net charge on the base the
same as that in all_nuc94.in. It is said that
differences bigger than 0.1 are likely due to errors
in the inputs, so I am including the gaussian input
file along with the resp input files (input files were
generated by antechamber, I modified the RESP inputs
to add the charge constraint).
Gaussian:
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2)
iop(6/42=6)
The structure is already optimized
0 1
N 2.055470 .915786 .000000 C .686292
.773862 .000000
C .343048 -.552488 .000000
N 1.509766 -1.236982 .000000
C 2.500180 -.282756 .000000
C -.359250 1.755612 .000000
N -1.620822 1.108796 .000000
C -1.837352 -.233152 .000000
N -.890976 -1.112274 .000000
N -3.122779 -.639015 .000000
O -.322786 2.949160 .000000
H -3.302019 -1.615975 .000000
H -3.888045 -.008030 .000000
H -2.393892 1.739352 .000000
H 3.534084 -.563481 .000000
C 1.664508 -2.674579 .000000
H 1.206542 -3.105048 .880243
H 1.206542 -3.105048 -.880243
H 2.719909 -2.908217 .000000
RESP1:
Resp charges for organic molecule
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
&end
1.0
Resp charges for organic molecule
0 19
7 0
6 0
6 0
7 0
6 0
6 0
7 0
6 0
7 0
7 0
8 0
1 0
1 12
1 0
1 0
6 0
1 0
1 0
1 0
4 0.1037
1 16 1 17 1 18 1 19
RESP2:
Resp charges for organic molecule
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
iqopt = 2,
qwt = 0.001,
&end
1.0
Resp charges for organic molecule
0 19
7 -99
6 -99
6 -99
7 -99
6 -99
6 -99
7 -99
6 -99
7 -99
7 -99
8 -99
1 -99
1 -99
1 -99
1 -99
6 0
1 0
1 17
1 17
4 0.1037
1 16 1 17 1 18 1 19
I really don't know what's going on, surely there must
be a mistake somewhere. Please I need your help. I
would be most grateful if you could help me sort this
problem out, any suggestion you could give me would be
highly appreciated. Thank you.
Laura.
__________________________________
Start your day with Yahoo! - Make it your home page!
http://www.yahoo.com/r/hs
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Nov 14 2005 - 14:53:00 PST
