Hello Edith,
Thank you very much for your response and suggestions.
Finally I was able to make Aria do the calculations. In my cyclic peptide the first residue is GLY and the last one is PRO. Thus I could use the presidue PPG1 described in the standard topology and parameters files. In addition I had to modify the two files as following:
In run1/cns/protocols/generate.inp I added the patch:
patch PPG1
reference =-= (resid 55)
reference =+= (resid 1)
end
And in run1/cns/toppar/topallhdg5.3.pep I added the two lines:
first PPG1 tail + GLY end
last PPG1 head - PRO end
It seems the topology and parameters files in the run directory tree that were copied upon run setup from Aria installation directory are not replaced by Aria with my modified files even so in a project.xml I specified to use the modified files. So one needs manually to replace files with all modified files after the run directory tree is created.
Also, the .pep file has a line:
link PPG1 head - * tail + GLY end
that I initially thought would be sufficient to make a peptide bond but it was not enough, thus the above two additional lines are needed.
Best,
Vitaliy
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