AMBER Archive (2004)

Subject: AMBER: Improper dihedral

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Mon Jan 12 2004 - 08:23:22 CST


Despite the fact that I have the parameters for improper dihedrals in my
frcmod file, I load a PDB and when I use saveamberparm, leap doesn't
apply the improper dihedrals parameters to the topology file. What do I
have to do to have the impropers apllied??
The PDB file:

ATOM 1 C1 DMA 1 1.995 -0.007 -0.017
ATOM 2 C2 DMA 1 1.441 1.310 -0.010
ATOM 3 C3 DMA 1 0.091 1.496 0.001
ATOM 4 C4 DMA 1 -0.826 0.403 0.008
ATOM 5 C5 DMA 1 -0.265 -0.909 0.001
ATOM 6 C6 DMA 1 1.083 -1.111 -0.011
ATOM 7 N7 DMA 1 3.321 -0.205 -0.028
ATOM 8 C8 DMA 1 3.878 -1.555 -0.036
ATOM 9 C9 DMA 1 4.243 0.928 -0.034
ATOM 10 C10 DMA 1 -2.196 0.662 0.020
ATOM 11 C11 DMA 1 -3.249 -0.264 0.027
ATOM 12 C12 DMA 1 -4.541 0.175 0.039
ATOM 13 O13 DMA 1 -5.544 -0.679 0.047
ATOM 14 H14 DMA 1 -4.784 1.237 0.043
ATOM 15 H15 DMA 1 4.963 -1.493 -0.044
ATOM 16 H16 DMA 1 3.578 -2.111 0.857
ATOM 17 H17 DMA 1 3.564 -2.107 -0.926
ATOM 18 H18 DMA 1 5.264 0.556 -0.042
ATOM 19 H19 DMA 1 4.114 1.546 0.858
ATOM 20 H20 DMA 1 4.101 1.547 -0.924
ATOM 21 H21 DMA 1 -0.916 -1.776 0.005
ATOM 22 H22 DMA 1 1.459 -2.125 -0.016
ATOM 23 H23 DMA 1 2.091 2.176 -0.015
ATOM 24 H24 DMA 1 -0.301 2.509 0.006
ATOM 25 H25 DMA 1 -2.480 1.715 0.024
ATOM 26 H26 DMA 1 -3.076 -1.335 0.024
CONECT 1 2 6 7
CONECT 2 1 3 23
CONECT 3 2 4 24
CONECT 4 3 5 10
CONECT 5 4 6 21
CONECT 6 1 5 22
CONECT 7 1 8 9
CONECT 8 7 15 16 17
CONECT 9 7 18 19 20
CONECT 10 4 11 25
CONECT 11 10 12 26
CONECT 12 11 13 14
CONECT 13 12
CONECT 14 12
CONECT 15 8
CONECT 16 8
CONECT 17 8
CONECT 18 9
CONECT 19 9
CONECT 20 9
CONECT 21 5
CONECT 22 6
CONECT 23 2
CONECT 24 3
CONECT 25 10
CONECT 26 11
MASTER 0 0 0 0 0 0 0 0 26 0 26 0
END

The frcmod file:

Campo de forca para o DMACA no estado zwiterionico (base = gaff) deve
ser usado com SHAKE on
MASS
q1 12.01 0.00 igual ao ca mas diferenciando para fazer quinona
q2 12.01 0.00 idem
cd 12.01 0.00 igual ao cd do gaff
c3 12.01 0.00 igual ao c3 do gaff
c 12.01 0.00 igual ao c do gaff
nh 14.01 0.00 igual ao nh do gaff
o 16.00 0.00 igual ao o do gaff
h1 1.008 0.00 igual ao h1 do gaff
h4 1.008 0.00 igual ao h4 do gaff
ha 1.008 0.00 igual ao ha do gaff

BOND
q1-q2 473.7 1.43 igual ao ca-ca (todos se referem somente a
constante de forca)
q2-q2 473.7 1.36 idem
q1-nh 426.0 1.34 ca-nh
nh-c3 328.6 1.46
c3-h1 340.4 1.09
q2-ha 354.5 1.08 ca-ha
q1-cd 473.7 1.39 ca-ca
cd-cd 473.7 1.40 idem
cd-c 473.7 1.36 idem
c -o 468.1 1.32 c-oh
c -h4 354.5 1.09 c-hc ou ca-ha ou cd-ha
cd-ha 354.5 1.08

ANGLE
o -c -h4 53.1 121.9 ha-c -o
o -c -cd 68.2 123.8 cd-c -o
h4-c -cd 46.8 115.2 cd-c -ha
c -cd-ha 46.7 116.4 c -cd-ha
c -cd-cd 65.5 121.2 c2-cd-cd
ha-cd-cd 46.9 115.8 cd-cd-ha
cd-cd-q1 65.0 123.5 c2-cd-cd
q1-cd-ha 46.8 116.1 ca-cd-ha
cd-q1-q2 62.6 120.7 ca-ca-cd
q2-q1-q2 63.0 120.0 ca-ca-ca
nh-q1-q2 65.9 120.3 ca-ca-nh
q1-q2-q2 63.0 120.0 ca-ca-ca
q1-q2-ha 45.1 122.8 ca-ca-ha
q2-q2-ha 45.1 122.8 ca-ca-ha
q1-nh-c3 64.3 117.3 c3-nh-ca
c3-nh-c3 63.5 114.3
nh-c3-h1 49.5 111.5 hc-c3-nh
h1-c3-h1 39.3 109.4

DIHE
X -c -cd-X 4 8.7 180.0 2.0 X -c -c2-X
X -cd-cd-X 4 4.0 180.0 2.0
X -cd-q1-X 4 4.0 180.0 2.0 X -c2-cd-X
X -q1-q2-X 4 14.5 180.0 2.0 X -ca-ca-X
X -q2-q2-X 4 14.5 180.0 2.0 idem
X -q1-nh-X 4 4.2 180.0 2.0 X -ca-nh-X
X -nh-c3-X 6 0.0 0.0 2.0

IMPROPER
h4-o -c -cd 1.1 180.0 2.0 Using default value
ha-c -cd-cd 1.1 180.0 2.0 Using default value
ha-cd-cd-q1 1.1 180.0 2.0 Using default value
cd-q2-q1-q2 1.1 180.0 2.0 Using default value
ha-q1-q2-q2 1.1 180.0 2.0 Using default value
nh-q2-q1-q2 1.1 180.0 2.0 Using default value
q1-c3-nh-c3 1.1 180.0 2.0 Using default value

NONBON
h4 1.4090 0.0150
ha 1.4590 0.0150
h1 1.3870 0.0157
o 1.6612 0.2100
c 1.9080 0.0860
c3 1.9080 0.1094
cd 1.9080 0.0860
q1 1.9080 0.0860 igual a ca
q2 1.9080 0.0860 idem
nh 1.8240 0.1700

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu