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From AA to CG pdb
- virgimiguel
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9 years 11 months ago #3829
by virgimiguel
From AA to CG pdb was created by virgimiguel
Hi, I am following the tutorial on MARTINI page for Parametrizing a new molecule(
cgmartini.nl/cgmartini/index.php/parametrzining-new-molecule
). I have reached the steep 6 "Create CG simulation".
I have a new molecule I need to parametrizes. I have mapped my beads, calculated angles and bonded parameters from an All Atom md simulations of my molecule and constructed my itp
Now that I have my "newmolecule".itp, the next steep is to obtained the coarse grained pdb.
as stated in the tutorial, I should Extract one frame from my mapped trajectory obtained in steep 3 ("Coarse-grain target atomistic data")
now, when I tried to trjconv to my mapped.xtc I need a tpr file, but if I used the trp from my AA simulation I reached to the problem that the number of atoms in the tpr is larger than the number of atoms in the
mapped trajectory file which only contains the number of my mapped beads, and no pdb is extracted....
I do not realize how should I obtained my coarse grained pdb, if someone can give me a hint I would really appreciate it. Sincerely, Virginia.
I have a new molecule I need to parametrizes. I have mapped my beads, calculated angles and bonded parameters from an All Atom md simulations of my molecule and constructed my itp
Now that I have my "newmolecule".itp, the next steep is to obtained the coarse grained pdb.
as stated in the tutorial, I should Extract one frame from my mapped trajectory obtained in steep 3 ("Coarse-grain target atomistic data")
now, when I tried to trjconv to my mapped.xtc I need a tpr file, but if I used the trp from my AA simulation I reached to the problem that the number of atoms in the tpr is larger than the number of atoms in the
mapped trajectory file which only contains the number of my mapped beads, and no pdb is extracted....
I do not realize how should I obtained my coarse grained pdb, if someone can give me a hint I would really appreciate it. Sincerely, Virginia.
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- Clement
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9 years 11 months ago #3832
by Clement
Replied by Clement on topic From AA to CG pdb
Hi,
Once you have a satisfying mapping, the easiest way is to output center of masses of the atom you gather into bead. By that I mean you can specify with an index file which atom are together in a bead, and output the center of mass of this group; this will be your CG bead. You do that for your whole trajectory, or for one frame (which will output your CG molecule then). You can easily do that with g_traj included in GROMACS. Mmmmh... Am I clear here?
The angle and bond distributions must be extracted from this AA-to-CG mapped trajectory!
Good luck!
Once you have a satisfying mapping, the easiest way is to output center of masses of the atom you gather into bead. By that I mean you can specify with an index file which atom are together in a bead, and output the center of mass of this group; this will be your CG bead. You do that for your whole trajectory, or for one frame (which will output your CG molecule then). You can easily do that with g_traj included in GROMACS. Mmmmh... Am I clear here?
The angle and bond distributions must be extracted from this AA-to-CG mapped trajectory!
Good luck!
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