normal Terminal residues

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6 months 1 week ago #8036 by Raksha
Terminal residues was created by Raksha
I have been trying to coarse-grain a protein dimer using the Martini 3 beta-version. I observe that the last two residues of chain B are not coarse-grained. The .ssd also lacks secondary structure information for these residues.

The command I use is
./martinize -f all-atom.pdb -ff martini303v.partition -x cg.pdb -o cg.top -dssp <path to dssp>

Is there something I am doing wrong?

I also attempted to coarse grain the two chains independently and then concatenate them, but this results in high forces / steric clashes.

I have attached the all-atom and coarse-grained files for reference.


drive.google.com/file/d/1nTM384w6TQXPZBB...byL/view?usp=sharing

drive.google.com/file/d/1k8Yx5Fcwhqmvy4C...A19/view?usp=sharing

Thanks!

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6 months 1 week ago #8038 by jbarnoud
Replied by jbarnoud on topic Terminal residues
Hi Raksha,

Your command line looks OK. Try to rename the two terminal oxygens from OT1 and OT2 to O1 and O2, respectively. DSSP does not like OT1 and OT2 si it drops the terminal residue, which causes martinize to drop it as well.

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6 months 1 week ago #8040 by Raksha
Replied by Raksha on topic Terminal residues
Thank you Jonathan, it works :)

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