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  • lianaliana
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14 years 1 week ago #362 by lianaliana
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Hello.
How do I get a [mapping] section in my topology? I tried using pdb2gmx in the modified version of gromacs (the one used to reversed transformation) and I get this Fatal error:
Program pdb2gmx, VERSION 3.3.1
Source code file: pgutil.c, line: 131

Fatal error:
Atom H not found in residue 1 while adding mapping
Residue 1 is a N-terminal methionine. Can anyone help me?
Thanks.

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  • andrzej
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14 years 1 week ago #363 by andrzej
Replied by andrzej on topic Mapping
You have to use -ignh and -missing options , as written in the appendix of the paper. All the mapping information is in the *.rtp files of the forcefield, so in case smth is missing, You can put additional information in the [mapping] sections, separate for each aminoacid. Note that I put [mapping] sections only for two forcefields but its no problem to make it for others.

pdb2gmx -ignh -missing -f aa.gro -p aa.top

Andrzej

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  • lianaliana
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14 years 1 week ago #365 by lianaliana
Replied by lianaliana on topic Mapping
Thank You very much. The problem was solved. I'm running the SA now!!

Liana.

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13 years 9 months ago #387 by Justin
Replied by Justin on topic Mapping
How about mapping in the lipid topology file? We can find a mapping section at the end of the DPPC.itp file that is included in the tutorial package. How about other lipid molecules? For instance, the POPC has a unsaturated tail.

Justin

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13 years 9 months ago #388 by andrzej
Replied by andrzej on topic Mapping
When You have very long chains that can be divided to some "blocks" You could tweak the rtp files, normally with amino acids description, that are used by pdb2gmx, to describe the blocks. This way the procedure can be slightly faster. However standard lipids are small enough to fill the mapping by hand

Andrzej

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  • sumar
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8 years 6 months ago #5181 by sumar
Replied by sumar on topic Mapping
Hello..

I want to mapp rhamnolipid molecule into CG file,could you suggest me what kind of known fragments coud be using as Rhamnolipid templates in CG file?


Sumar

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8 years 6 months ago #5183 by Pim
Replied by Pim on topic Mapping
Perhaps octyl glucoside is a good starting point:
www.cgmartini.nl/index.php/force-field-p...urfactants&lipid=BOG

The double sugar may be inspired by the sugar force field:
www.cgmartini.nl/images/parameters/ITP/martini_v2.0_sugars.itp

Also, the tutorial for parameterizing a new molecule describes a sugar unit connected to a long tail, this may serve as inspiration for your mapping and parameters, as well as the procedure to validate it.
www.cgmartini.nl/index.php/tutorials-gen...rzining-new-molecule

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8 years 6 months ago - 8 years 6 months ago #5213 by sumar
Replied by sumar on topic Mapping
tanks

I have tried using BOG file (just for BOG not for rham), but I got error when I simulation. there are notif that I got
Warning: atom name 1 in sistem.top and solvate.gro does not match (B1 - P1)
Warning: atom name 2 in sistem.top and solvate.gro does not match (B2 - P4)
Warning: atom name 3 in sistem.top and solvate.gro does not match (B3 - P2)
Warning: atom name 5 in sistem.top and solvate.gro does not match (C2 - C1)
Warning: atom name 6 in sistem.top and solvate.gro does not match (B1 - P1)
Warning: atom name 7 in sistem.top and solvate.gro does not match (B2 - P4)
Warning: atom name 8 in sistem.top and solvate.gro does not match (B3 - P2)

while in BOG file I see that
1 P1 1 BOG B1 1 0 60.0528
2 P4 1 BOG B2 2 0 60.0528
3 P2 1 BOG B3 3 0 60.0528
4 C1 1 BOG C1 4 0
5 C1 1 BOG C2 5 0

so I got Confused, Why P1 doesn't match with B1, and so on..
could you suggest me whats wrong with my files?


tks
sumar
Last edit: 8 years 6 months ago by sumar.

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8 years 5 months ago #5215 by helgi
Replied by helgi on topic Mapping
In the BOG .itp file the second row is the bead type (P1, P4, etc) which are defined in the main Martini .itp file the fifth row is the atom name – which is not used by GROMACS. Most often used for visualization and/or help with selecting indexes etc.

When the names don’t match in the .gro and .itp files grompp give you an warning not an error – and if the atoms and atom ordering is correct you can ignore it.

Cheers,
- Helgi

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