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Parameterizing a new molecule
- ywang52
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7 years 10 months ago #5722
by ywang52
Parameterizing a new molecule was created by ywang52
Hi All
I am very new here. I am trying to run an amphiphilic polymer with MARTINI. As it is a new molecule, I am now learning to parameterize it first.
My question is, is that possible to generate the topology for the new molecule by "pbd2gmx" from an rtp file, or do I have to write the whole itp file for the molecule?
Thanks very much!
Yang
I am very new here. I am trying to run an amphiphilic polymer with MARTINI. As it is a new molecule, I am now learning to parameterize it first.
My question is, is that possible to generate the topology for the new molecule by "pbd2gmx" from an rtp file, or do I have to write the whole itp file for the molecule?
Thanks very much!
Yang
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- peterkroon
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7 years 10 months ago #5723
by peterkroon
Replied by peterkroon on topic Parameterizing a new molecule
Hi and welcome :)
pdb2gmx can only help you with making atomistic topologies, as far as I know.
What you could try (since you have a polymer) is creating a coarse grained conformation (pdb), and feed that to pdb2gmx with an appropriate rtp, but there is a lot of dark magic in pdb2gmx, so I don't know if this will work.
See also: cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5
pdb2gmx can only help you with making atomistic topologies, as far as I know.
What you could try (since you have a polymer) is creating a coarse grained conformation (pdb), and feed that to pdb2gmx with an appropriate rtp, but there is a lot of dark magic in pdb2gmx, so I don't know if this will work.
See also: cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5
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- ywang52
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7 years 9 months ago #5742
by ywang52
Replied by ywang52 on topic Parameterizing a new molecule
Thank you! I agree with you, I wrote the itp by hand, and now it works.
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