Dear Amber Users!
There are some questions about parametrization of the non-standart amino
acids (using simplest antechamber method) and its further connection to the
rest of the backbone.
Should the initial pdb of the non standard residue be consisted of capped N
and C termi with NH2 and COOH groups or alternatively with NH and CO? I've
tried to parametrize the whole residue with both types of caps but
eventually after its integration to the rest of the protein using
source leaprc.ff99SB
source leaprc.gaff
loadoff crq.lib
loadamberparams crq.frcmod
protein = loadpdb protein_with_crq.pdb
bond protein.62.C protein.63.N1
bond protein.63.C3 protein.66.N
as the result the additional OXT and H atoms always have been wrongly added
to the previous (62) and next (66) residues so the geometry of new two
peptide bonds have been perturbed. How I could fix it?
James
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Received on Fri May 30 2014 - 11:30:02 PDT
