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g_fg2cg with martini 2.2P
- nanogod
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11 years 4 months ago #1315
by nanogod
g_fg2cg with martini 2.2P was created by nanogod
I have problems with reverse transformation of a solvated protein I simulated with martini 2.2P ff and after countless attempts I am just wondering if it possible with martini 2.2P?
Kind regards
Nanogod
Kind regards
Nanogod
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- djurre
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11 years 4 months ago #1316
by djurre
Replied by djurre on topic g_fg2cg with martini 2.2P
The short answer: I don't know.
I would expect it to work when for the mapping nothing is mapped to the dummy particles inside charge/polar beads and water. However I don't know if the cg2fg code can handle that. And what happens if you run the backmapping simulation with the fg particles constrained to the CG system.
A work around would be to remove those from your CG gro/pdb file first. For example do a "grep -v D CG.gro > CG-noD.gro".
If that doesn't solve your problem: what kind of error do you get?
I would expect it to work when for the mapping nothing is mapped to the dummy particles inside charge/polar beads and water. However I don't know if the cg2fg code can handle that. And what happens if you run the backmapping simulation with the fg particles constrained to the CG system.
A work around would be to remove those from your CG gro/pdb file first. For example do a "grep -v D CG.gro > CG-noD.gro".
If that doesn't solve your problem: what kind of error do you get?
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- nanogod
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11 years 4 months ago #1318
by nanogod
Replied by nanogod on topic g_fg2cg with martini 2.2P
Hey djurre, you will soon receive a more thorough email, from my college, about the problem and what we have done :)
But, when I do as in the guide with the 2.2P i either end up with a fully translated fg structure with no coordinates, when I use -wat 1 in the g_fg2cg commando, when I dont use the -wat 1 command I get a translation but only with as many molecules as in the CG structure and with no koordinates.
But, when I do as in the guide with the 2.2P i either end up with a fully translated fg structure with no coordinates, when I use -wat 1 in the g_fg2cg commando, when I dont use the -wat 1 command I get a translation but only with as many molecules as in the CG structure and with no koordinates.
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