XUEMING TANG wrote:
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
An unfortunate practice. PRODRG topologies are questionable, at best, and often
the time is not taken to properly refine them, or at least describe what changes
were made when writing methodology.
forcefield is gromos which is outdated.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
All of this depends on what you mean by "GROMOS" force field. There are many
such parameter sets. The original PRODRG was based on GROMOS87, which is indeed
extremely outdated. The PRODRG 2.5 (beta) server supports GROMOS96 43A1, but
the same caveat applies as far as accuracy. At least it's based on a newer
force field.
Unfortunately, "shortcuts" taken during parameterization usually leave you with
junk in the topology. Parameterizing new species is very time-consuming, if
done properly.
calculated by prodrg is inaccurate.
Additional question, would G53a6 is basically better than G45a3 for SDS?
There are a number of papers that have done simulations with SDS. You should
probably base your force field choice on what you find in the literature.
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.
You're comparing different force fields, so yes, there will be differences. If
you're planning to constrain all bonds, then the force constants there are not
significant and aren't used (they apply to a quartic potential). Otherwise, use
parameters that consistently originate from one force field parameter set. If
you can't find certain parameters, then you should consider your force field
choice more thoroughly.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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