normal Tryptophan Mapping

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1 year 9 months ago #8508 by z.sichaib
Tryptophan Mapping was created by z.sichaib
Dear Martini users,

I am trying to parametrize a new molecule. One of its fragments is a tryptophan structurally related molecule.

I'm trying to assign atom-to-bead at Tryptophan side chain but I am a little bit confused.

If I follow the mapping file "trp.charmm36.map" the atom-to bead representation should be:

[SC1]
CB CG CD1 NE1
[SC2]
NE1 CE2 CD2 CZ2 CH2
[SC3]
CG CE2 CD2 CE3 CZ3
[SC4]
CE3 CZ3 CZ2 CH2

but this is not a 2 (or 3) to 1 bead?!

I found another mapping here (page 5): www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf

And another different one here:
www.cgmartini.nl/index.php/component/kun...4-tryptophan-mapping

Can you please confirm which is the correct one?

I would really appreciate your help.

Zeineb

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1 year 8 months ago #8509 by riccardo
Replied by riccardo on topic Tryptophan Mapping
Well, it's not that beads include 5 heavy atoms since most of the atoms are repeated (i.e., mapped) into more than one bead. This means that, e.g., bead SC1 represents CB, 1/2 CG, CD1 and 1/2 NE1, SC2 1/2 NE1, 1/2 CE2, 1/2 CD2, 1/2 CH2, and 1/2 CZ2, etc.
As a consequence, the SC1 bead actually represents 2+1/2+1/2=3 non-hydrogen atoms, SC2 2.5 non-hydrogen atoms, etc.


Personally, in such cases I define the index in the following way:
[SC1]
CB CB CG CD1 CD1 NE1
[SC2]
NE1 CE2 CD2 CZ2 CH2
[SC3]
CG CE2 CD2 CE3 CZ3
[SC4]
CE3 CZ3 CZ2 CH2

where, with the repetition of the "CB" and "CD1" atoms in the SC1 bead (the only ones which are not shared according to this mapping), I give to such atoms a 2 x weight in determining the position of the SC1 bead.

Regarding which mapping is the right one, I would trust the one from backward, especially if taken from the GitHub repo ( github.com/Tsjerk/Backward/blob/master/Mapping/trp.charmm36.map ).

Hope this helps and I will reply about isoquinoline in the other thread.

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1 year 8 months ago #8527 by z.sichaib
Replied by z.sichaib on topic Tryptophan Mapping
Dear Riccardo, Thank you so much for your explanation, I understand the principle of Mapping better now. I appreciate!
Yes, I used the one from the GitHub repository.

There is still something not clear to me. When I followed this mapping, the resulting CG molecule didn't seem correct to me so I went back to the original Martini paper and I found this:

The Mapping of TRP in Martini2.2 is:
SC4-SNd-SC5-SC5

SC4: Cβ-Cγ-Cδ2
SNd: Cδ1-Nε-Cε1
SC4/5: Cε2-Cξ2
SC4/5: Cε1-Cω

Usually, the nomenclature of TRP atoms is CB, CG, CD1, NE1, CE2, CD2, CE3, CZ3, CH2, CZ2, ( ligand-expo.rcsb.org/reports/T/TRP/TRP_D3L1.gif ) but there is no Cε1 (CE1) or Cω?

Thus, I can't understand the mapping given in the Martini paper (Table2) here: cgmartini.nl/images/stories/martini-chapter.pdf

I would appreciate your help on this :)

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1 year 7 months ago #8573 by riccardo
Replied by riccardo on topic Tryptophan Mapping
You're welcome :) and sorry for the slow follow up.

Well, using the nomenclature of ligand-expo.rcsb.org/reports/T/TRP/TRP_D3L1.gif , I'd say the mapping is:

SC4: CB-CG-CD2    (basically same nomenclature, just latin vs greek)
SNd: CD1-NE1-CE2 (very similar nomenclature)
SC4/5: CE3-CZ3  (basically same nomenclature)
SC4/5: CH2-CZ2 (the remaining 2 carbons of the TRP)

I guess here ( cgmartini.nl/images/stories/martini-chapter.pdf ) they are using a (slightly) different nomenclature. I am not really familiar with amino acid atom nomenclatures so cannot really tell more.

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