[gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3
XUEMING TANG
yujan2007 at gmail.com
Wed Feb 9 20:14:42 CET 2011
Hi there
This is maybe an old question. I want to ask a general procedure of generate
topology file with gromo96 force field by Dundee Prodrg. Take SDS for an
example, I want to use gromos96 G45a3 forcefield. After the file is
generated by dundee, I compare the forcefield parameter of G45a3 with what
Dundee output for(bond length, angle, dihedral, imp, potential). There are
some differences (see below). While from papers author usually just
mentioned that the file is generated by Prodrg without detailed information.
According to Dundee website, the forcefield is gromos which is outdated.
Should I change all the forcefield parameter by hand for any molecule I want
to use with gromos ff. Or there is any shortcut I can try. I understand that
charge calculated by prodrg is inaccurate.
Additional question, would G53a6 is basically better than G45a3 for SDS?
DundeePRo ff45a3
Length Potential Length Potential
CHn-CHn 0.153 3.35E+05 0.153 7.15E+06
C-SO1 0.143 2.51E+05 0.143 8.18E+06
SO1-S 0.143 3.35E+05
S-SO2 0.143 3.35E+05
S=SO3 0.15 3.77E+05 0.15 8.37E+06
S=SO4 0.15 3.77E+05 0.15 8.37E+06
angle Potential angle Potential
C-C-C 111 460.2 111 530
C-C-SO1 109.5 460.2 109.5 520
C-SO1-S 120 397.5
SO1-S-SOn 109.5 460.2
dihedral Potential dihedral Potential
S-SO1-SO3-SO2 35.3 836.8 35.3 334.8
C-C-C-C 0 5.9 3
SO1-C-C-C 0 5.9 3
S-SO1-C1-C2 0 3.8 3 0 1.3 3
C1-SO1-S-SO4 0 1.3 3
~
Mainly the potential is different. And I didnot find the exact value on the
blank parts in ff45a3 categories.
File generated by Dundee:
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.153 334720.0 0.153 334720.0 ; C12 C11
2 3 2 0.153 334720.0 0.153 334720.0 ; C11 C10
3 4 2 0.153 334720.0 0.153 334720.0 ; C10 C9
4 5 2 0.153 334720.0 0.153 334720.0 ; C9 C8
5 6 2 0.153 334720.0 0.153 334720.0 ; C8 C7
6 7 2 0.153 334720.0 0.153 334720.0 ; C7 C6
7 8 2 0.153 334720.0 0.153 334720.0 ; C6 C5
8 9 2 0.153 334720.0 0.153 334720.0 ; C5 C4
9 10 2 0.153 334720.0 0.153 334720.0 ; C4 C3
10 11 2 0.153 334720.0 0.153 334720.0 ; C3 C2
11 12 2 0.153 334720.0 0.153 334720.0 ; C2 C1
12 13 2 0.143 251040.0 0.143 251040.0 ; C1 SO1
13 14 2 0.143 334720.0 0.143 334720.0 ; SO1 S
14 15 2 0.143 334720.0 0.143 334720.0 ; S SO2
14 16 2 0.150 376560.0 0.150 376560.0 ; S SO3
14 17 2 0.150 376560.0 0.150 376560.0 ; S SO4
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; C12 C9
2 5 1 ; C11 C8
3 6 1 ; C10 C7
4 7 1 ; C9 C6
5 8 1 ; C8 C5
6 9 1 ; C7 C4
7 10 1 ; C6 C3
8 11 1 ; C5 C2
9 12 1 ; C4 C1
10 13 1 ; C3 SO1
11 14 1 ; C2 S
12 15 1 ; C1 SO2
12 16 1 ; C1 SO3
12 17 1 ; C1 SO4
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 111.0 460.2 111.0 460.2 ; C12 C11 C10
2 3 4 1 111.0 460.2 111.0 460.2 ; C11 C10 C9
3 4 5 1 111.0 460.2 111.0 460.2 ; C10 C9 C8
4 5 6 1 111.0 460.2 111.0 460.2 ; C9 C8 C7
5 6 7 1 111.0 460.2 111.0 460.2 ; C8 C7 C6
6 7 8 1 111.0 460.2 111.0 460.2 ; C7 C6 C5
7 8 9 1 111.0 460.2 111.0 460.2 ; C6 C5 C4
8 9 10 1 111.0 460.2 111.0 460.2 ; C5 C4 C3
9 10 11 1 111.0 460.2 111.0 460.2 ; C4 C3 C2
10 11 12 1 111.0 460.2 111.0 460.2 ; C3 C2 C1
11 12 13 1 109.5 460.2 109.5 460.2 ; C2 C1 SO1
12 13 14 1 120.0 397.5 120.0 397.5 ; C1 SO1 S
13 14 15 1 109.5 460.2 109.5 460.2 ; SO1 S SO2
13 14 16 1 109.5 460.2 109.5 460.2 ; SO1 S SO3
13 14 17 1 109.5 460.2 109.5 460.2 ; SO1 S SO4
15 14 16 1 109.5 460.2 109.5 460.2 ; SO2 S SO3
15 14 17 1 109.5 460.2 109.5 460.2 ; SO2 S SO4
16 14 17 1 109.5 460.2 109.5 460.2 ; SO3 S SO4
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
14 13 16 15 2 35.3 836.8 35.3 836.8 ; imp S SO1 SO3
SO2
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C10
C11 C12
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C8 C9 C10
C11
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C7 C8 C9
C10
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C6 C7 C8
C9
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C5 C6 C7
C8
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C5 C6
C7
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C3 C4 C5
C6
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C2 C3 C4
C5
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C1 C2 C3
C4
13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih SO1 C1 C2
C3
14 13 12 11 1 0.0 3.8 3 0.0 3.8 3 ; dih S SO1 C1
C2
12 13 14 17 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 SO1 S
SO4
Thank you for your time!
Best!
Xueming
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