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unanswered Using initram.sh with peptides with capped termini

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9 years 11 months ago #3793 by clavila
Using initram.sh with peptides with capped termini was created by clavila
Dear all,
I would like to use the backward transformation tool on a peptide that has a capped termini, i.e. the negative charge in the carboxi termini is neutralized with a NH2. In the coarse grained structure I have manually adjusted the charge of the last backbone atom to 0 instead of -1. I noticed that the backward.py script is able to parse the residue NH2, but on one hand in the Mapping directory there is no mapping information for this residue, and on the other hand the NH2 "residue" is not explicitely specified in the CG configuration/topology files as stated before.
I would deeply appreciate any suggestions on how to proceed in this case.

Cheers,
Cesar

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