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MnEDTA
- schmidt.nedlitz
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12 years 10 months ago #676
by schmidt.nedlitz
MnEDTA was created by schmidt.nedlitz
Hey Martini community,
I just created a topology file for EDTA bound to Mn2+, anyway I first wanted to check if the topology file is right designed before adding it to the topology library of this side, since I had issues with the chelating group in how it is bound to the 2 Nitrogen and the four carboxyl groups. Also another issue was how to present a ion in close contact with EDTA. from the aa structure we know that the bond length from N to Mn is 1.9 and from the binding O to Mn is 1.8 A. see below for the EDTA topology.
[ moleculetype]
; molname nrexcl
EDTA 1
[atoms]
;id type resnr redidu atom cgnr charge mass
1 Qd 1 EDTA Mn1 1 +2
2 Na 1 EDTA RN1 2 0
3 Na 1 EDTA RN2 3 0
4 Qa 1 EDTA CO1 4 -1
5 Qa 1 EDTA CO2 5 -1
6 Qa 1 EDTA CO3 6 -1
7 Qa 1 EDTA CO4 7 -1
[bonds]
; i j funct length force.c
2 3 1 0.47 1250
3 4 1 0.47 1250
3 5 1 0.47 1250
2 6 1 0.47 1250
2 7 1 0.47 1250
1 2 1 0.50 1250
1 3 1 0.50 1250
1 4 1 0.47 1250
1 5 1 0.47 1250
1 6 1 0.47 1250
1 7 1 0.47 1250
;
;nonstandard bonds
;
;[constrains]
; i j funct length forcec.
[angles]
; i j k funct angle forcec. multiplic.
5 3 4 2 110 24
6 2 7 2 110 24
;;;;; Mn1 represents the ion (+2), RN1 and RN2 are N-CH2, CO1-4 are COO-CH2 (-1)
;;;;; I represented the ionic bonds pretty much just like normal covalent bonds, such i was wondering if there is anotherway of presentation.
Thank you so much, I hope to hear from you.
Thomas
I just created a topology file for EDTA bound to Mn2+, anyway I first wanted to check if the topology file is right designed before adding it to the topology library of this side, since I had issues with the chelating group in how it is bound to the 2 Nitrogen and the four carboxyl groups. Also another issue was how to present a ion in close contact with EDTA. from the aa structure we know that the bond length from N to Mn is 1.9 and from the binding O to Mn is 1.8 A. see below for the EDTA topology.
[ moleculetype]
; molname nrexcl
EDTA 1
[atoms]
;id type resnr redidu atom cgnr charge mass
1 Qd 1 EDTA Mn1 1 +2
2 Na 1 EDTA RN1 2 0
3 Na 1 EDTA RN2 3 0
4 Qa 1 EDTA CO1 4 -1
5 Qa 1 EDTA CO2 5 -1
6 Qa 1 EDTA CO3 6 -1
7 Qa 1 EDTA CO4 7 -1
[bonds]
; i j funct length force.c
2 3 1 0.47 1250
3 4 1 0.47 1250
3 5 1 0.47 1250
2 6 1 0.47 1250
2 7 1 0.47 1250
1 2 1 0.50 1250
1 3 1 0.50 1250
1 4 1 0.47 1250
1 5 1 0.47 1250
1 6 1 0.47 1250
1 7 1 0.47 1250
;
;nonstandard bonds
;
;[constrains]
; i j funct length forcec.
[angles]
; i j k funct angle forcec. multiplic.
5 3 4 2 110 24
6 2 7 2 110 24
;;;;; Mn1 represents the ion (+2), RN1 and RN2 are N-CH2, CO1-4 are COO-CH2 (-1)
;;;;; I represented the ionic bonds pretty much just like normal covalent bonds, such i was wondering if there is anotherway of presentation.
Thank you so much, I hope to hear from you.
Thomas
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