normal Mapping for an azide group

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7 years 7 months ago #5824 by ywang52
Mapping for an azide group was created by ywang52
Hi

I am trying to parameterizing a molecule that contains a 5 unit ring structure with an azide group in it. I've tried couple of ways to map it, but with the goal of reproducing the distributions obtained from all atom simulation, I still can't get it right (actually far from right). As far as I know from the original MARTINI paper, there is no such a bead which represents for azide group. So, can any of you recommend me a way of mapping this structure?

Thanks very much!

Below is the best draw I can do here. Thanks again!

C
|
N-N=N
\ /
C=C
|
C

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7 years 7 months ago - 7 years 7 months ago #5826 by ywang52
Replied by ywang52 on topic Mapping for an azide group
Hi, Sorry that the previous one was so unclear. I tried it again, I use "." to fill up the space, so you can just ignore those "."

Thanks again!

C
.|
N-N=N
\......../
.C=C
..|
.C
Last edit: 7 years 7 months ago by ywang52.

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7 years 7 months ago #5829 by riccardo
Replied by riccardo on topic Mapping for an azide group
Hi,
which distributions in particular you haven't managed to reproduce - which mappings have you tried?
If this is the whole molecule I would map it like this

(S-)bead # 1: C-N (SP3)
(S-)bead # 2: N=N (SP4/SP5)
(S-)bead # 3: C-C=C (SC4/SC5)

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If it's part of a bigger molecule you may want to group more atoms together (thus having fewer 2-atoms beads).

Regarding the bead types, those I indicated are only tentative. I recommend to look in the literature for previously mapped molecules with similar groups and experimental partitioning data to find the best bead types. Also other suggestions from the forum are most welcome

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7 years 7 months ago #5830 by ywang52
Replied by ywang52 on topic Mapping for an azide group

riccardo wrote: Hi,
which distributions in particular you haven't managed to reproduce - which mappings have you tried?
If this is the whole molecule I would map it like this

(S-)bead # 1: C-N (SP3)
(S-)bead # 2: N=N (SP4/SP5)
(S-)bead # 3: C-C=C (SC4/SC5)



If it's part of a bigger molecule you may want to group more atoms together (thus having fewer 2-atoms beads).

Regarding the bead types, those I indicated are only tentative. I recommend to look in the literature for previously mapped molecules with similar groups and experimental partitioning data to find the best bead types. Also other suggestions from the forum are most welcome


Hi Riccardo

Thank you very much. Yes, this is part of the molecule I try to parameterize, other parts are pretty straightforward, those distributions I had trouble to reproduce were all related to this part. I did the mapping the same way as you did, but I used SNa and SNd as the bead #1 and bead #2, I will try SP beads and see if they can give me better results.

I really appreciate your suggestion.

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7 years 7 months ago #5837 by xavier
Replied by xavier on topic Mapping for an azide group
I believe that the distribution in a 3 bead ring should be straightforward! The beads should be excluded from each other so just fit to the ref distance. You may have interference from the rest of the molecule that is attached ... expulsions might help.

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7 years 7 months ago #5846 by riccardo
Replied by riccardo on topic Mapping for an azide group

ywang52 wrote: Thank you very much. Yes, this is part of the molecule I try to parameterize, other parts are pretty straightforward, those distributions I had trouble to reproduce were all related to this part. I did the mapping the same way as you did, but I used SNa and SNd as the bead #1 and bead #2, I will try SP beads and see if they can give me better results.


Changing from SNa/d to SP beads will not affect intra-ring bond/angle distributions. Like Xavier suggests, you may have some interference from the rest of the molecule, in which case excluding some nonbonded interactions between some of the ring beads and beads from the rest of the molecule might help.

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