[gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

MD refmac5 at gmail.com
Mon Jan 15 19:34:46 CET 2018

Hi Gromacs folks,

I have a modified amino acid which has all the parameters set. However, the
last error is the "cmap torsion between atoms xxxxxxx" and it would't go
away. Basically the cmap contains atoms of  C-N-CA-C-N from three residues,
where the CA is my newly modified residue. THe only thing I could think of
is the newly modified residue was not recognized by gromacs, but I have
checked the residue.dat, the log from pdb2gmx and it looks like this
residue was not considered "alien". Got stuck here any help will be



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