normal Problem determining mapping coordinates for atom C3 of residue POPC

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1 week 1 day ago - 1 week 1 day ago #7922 by z.sichaib
z.sichaib created the topic: Problem determining mapping coordinates for atom C3 of residue POPC
Dear Martini Users,

I'm trying to backmap a system consisting of Protein + Water + Ions + POPC + POPE + CHOL using backward (I downloaded the latest version from Github: github.com/Tsjerk/Backward ).

./initram.sh -f Frame10.gro -o Frame10_aa.gro -to amber -p topol.top

For the mapping file, I just renamed 'popc.charmm36.map' to 'popc.amber.map' (The number of beads is 12, I checked the atoms/beads names in the .itp files and .map file and everything seems correct) but still I'm getting the following error:
Residues defined for transformation from martini to amber:
['POPC', 'ILE', 'POPG', 'GLN', 'POPS', 'GLY', 'POPE', 'GLU', 'CYS', 'HIS', 'SER', 'LYS', 'PRO', 'CHOL', 'TOCL2', 'GM1', 'ASN', 'VAL', 'DPPC', 'DOPC', 'THR', 'ASP', 'TRP', 'PHE', 'ALA', 'MET', 'LEU', 'ARG', 'TYR']
Problem determining mapping coordinates for atom C3 of residue POPC.
Atomlist:
['C3', 'O3', "H3'", 'H3', 'C4', 'H4A', 'H4B', 'C5', 'C6', 'H6', 'C7', 'H7A', 'H7B', 'C8', 'H8', 'C14', 'H14', 'C15', 'H15A', 'H15B', 'C16', 'H16A', 'H16B', 'C17', 'H17', 'C13', 'C18', 'H18A', 'H18B', 'H18C', 'C12', 'H12A', 'H12B', 'C11', 'H11A', 'H11B', 'C9', 'H9', 'C10', 'C19', 'H19A', 'H19B', 'H19C', 'C1', 'H1A', 'H1B', 'C2', 'H2A', 'H2B', 'C20', 'H20', 'C21', 'H21A', 'H21B', 'H21C', 'C22', 'H22A', 'H22B', 'C23', 'H23A', 'H23B', 'C24', 'H24A', 'H24B', 'C25', 'H25', 'C26', 'H26A', 'H26B', 'H26C', 'C27', 'H27A', 'H27B', 'H27C']
Trying to determine coordinates for particle:
C3
These coordinates should map from particles:
['ROH', 'ROH', 'ROH', 'R1']
At this step the following particles are available:
['C1B', 'C1A', 'NC3', 'C3A', 'C3B', 'C2B', 'C4A', 'C4B', 'D2A', 'GL1', 'GL2', 'PO4']
Bailing out...
['C3', 'O3', "H3'", 'H3', 'C4', 'H4A', 'H4B', 'C5', 'C6', 'H6', 'C7', 'H7A', 'H7B', 'C8', 'H8', 'C14', 'H14', 'C15', 'H15A', 'H15B', 'C16', 'H16A', 'H16B', 'C17', 'H17', 'C13', 'C18', 'H18A', 'H18B', 'H18C', 'C12', 'H12A', 'H12B', 'C11', 'H11A', 'H11B', 'C9', 'H9', 'C10', 'C19', 'H19A', 'H19B', 'H19C', 'C1', 'H1A', 'H1B', 'C2', 'H2A', 'H2B', 'C20', 'H20', 'C21', 'H21A', 'H21B', 'H21C', 'C22', 'H22A', 'H22B', 'C23', 'H23A', 'H23B', 'C24', 'H24A', 'H24B', 'C25', 'H25', 'C26', 'H26A', 'H26B', 'H26C', 'C27', 'H27A', 'H27B', 'H27C']


Here, you can find the .itp, .map, .topol and .gro files that I'm using.
www.dropbox.com/sh/ntssunjjh9d8s4i/AACs-...xofvV5WBVOEDpwa?dl=0

I checked everything and still can't find the problem... Any help, please.
Last Edit: 1 week 1 day ago by z.sichaib.

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6 days 12 hours ago #7929 by z.sichaib
z.sichaib replied the topic: Problem determining mapping coordinates for atom C3 of residue POPC
I'm really out of ideas...

- The mapping file of POPC seems correct.
- I included the atomistic topology of POPC and this latter seems in concordance with the information in the mapping file.
- The atoms' name in the input file (.gro) are the same as in the mapping file and the .itp file of POPC

Still, I can't understand why there is a "problem determining mapping coordinates for atom C3 of residue POPC"

If someone already backmapped POPC molecules from Martini to Amber, I would really appreciate his help.

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6 days 12 hours ago - 6 days 12 hours ago #7930 by riccardo
riccardo replied the topic: Problem determining mapping coordinates for atom C3 of residue POPC
I think I found the problem. The hint was that backward says:

These coordinates should map from particles:
['ROH', 'ROH', 'ROH', 'R1']

which means that it expects C3 mapping to ROH & R1... which are however beads of CHOL. So I found that there's a mismatch between your gro and top, namely, in the gro file you have the following order: protein, POPC, POPE, and CHOL, while in the top you have:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
CHOL              135
POPC              150
POPE              198

Ordering in the gro and top should match, of course.! Fix the order in the top and try again. I think this should fix it.

Hope this helps!
Last Edit: 6 days 12 hours ago by riccardo.

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6 days 9 hours ago - 3 days 10 hours ago #7931 by z.sichaib
z.sichaib replied the topic: Problem determining mapping coordinates for atom C3 of residue POPC
Hi Riccardo,

Yes, you were right! I changed the order of the molecules in the top file and it fixed the problem :D
Thank's alot
Last Edit: 3 days 10 hours ago by z.sichaib.

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