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- How can I generate a topology for a peptide contain unnatural amino acids and a
How can I generate a topology for a peptide contain unnatural amino acids and a
- Kalindu
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2 years 3 months ago #9283
by Kalindu
How can I generate a topology for a peptide contain unnatural amino acids and a was created by Kalindu
Dear Martini users,
I have a peptide with two unnatural amino acids. How do I generate topology files for the MD simulation in Martini ?
Thank you in advance !
I have a peptide with two unnatural amino acids. How do I generate topology files for the MD simulation in Martini ?
Thank you in advance !
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- xavier
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2 years 3 months ago #9284
by xavier
Replied by xavier on topic How can I generate a topology for a peptide contain unnatural amino acids and a
Hi,
To generate the topology for a peptide which has two unnatural (non-conventional) aminoacides you need first to define the unnatural amino acids.
The easiest manner to do so is by using exciting AAs. The bonded terms can be defines as for natural AAs paying extreme attention to physics properties (motions). Using an all atom version first might be helpful. The chemical properties should also be preserved. The choice is bead type would define them and they should preserve the properties.
It is a non-trivial operation but prepared carefully it should be worth it.
Once the unnatural-AAs are defined (as any conventional AAs, different names in the several files), they also need to be defined in martinize to be treated as conventional AA.
Then and only then a peptide topology can be generated with the usual steps.
It is a simple procedure in principe but should be operated with care and previous experience would help :)).
Good luck.
To generate the topology for a peptide which has two unnatural (non-conventional) aminoacides you need first to define the unnatural amino acids.
The easiest manner to do so is by using exciting AAs. The bonded terms can be defines as for natural AAs paying extreme attention to physics properties (motions). Using an all atom version first might be helpful. The chemical properties should also be preserved. The choice is bead type would define them and they should preserve the properties.
It is a non-trivial operation but prepared carefully it should be worth it.
Once the unnatural-AAs are defined (as any conventional AAs, different names in the several files), they also need to be defined in martinize to be treated as conventional AA.
Then and only then a peptide topology can be generated with the usual steps.
It is a simple procedure in principe but should be operated with care and previous experience would help :)).
Good luck.
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