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13 years 3 months ago #456 by Kargar
Can I do the coarse graining for this peptide? was created by Kargar
Dear All Martini's Users

I did an atomistic peptide simulation. The sequences and positions of all atom in this peptide created by my self, I mean I didn't download the pdb file from < www.pdb.org >. at the end of atomistic simulation I have .pdb and .gro files that show the minimized structure of the peptide.

Now I have a question: Can I use the last pdb file for a CG peptide? Can I use atom2cg.awk and seq2itp.pl in this case?

Thank you
Kargar

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13 years 3 months ago #460 by xavier
Replied by xavier on topic Can I do the coarse graining for this peptide?
Technically speaking it would be possible to use the final structure (pdb or gro) or your atomistic simulation. However, it is important that you realize that the topology will be function of the secondary structure of the peptide in that last conformation. (The secondary structure will not be able to change during the simulation.) This will certainly affect the sampling of your peptide.

XAvier.

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