pdb2gmx does not generate cmap entries for alanine dipeptide
While processing a pdb containing the alanine dipeptide (ALAD), pdb2gmx does not generate the cmap entry in the topology file, although it is listed on the RTP.
Fixed CMAP generation for alanine dipeptide special residue
Fix CMAP to work for residues not detected as proteins, and
make sure we correctly process single-residue entries that
have residue-internal CMAP definitions. In particular, this
is important for the default alanine dipeptide special
residues (ALAD) in Charmm27.
#2 Updated by Justin Lemkul over 6 years ago
Roland Schulz wrote:
As you wrote on the mailing-list, all CMAP entries refer to the previous and the next residue. Thus no matching entry exists for a di-peptide. Should a di-peptide have a CMAP entry?
In aminoacids.rtp of the latest charmm27.ff (in release-4-6), there is an alanine dipeptide (ALAD) entry, which has a [cmap] directive. Is the directive somehow not working, or is your input specifying something else?
#10 Updated by Rossen Apostolov almost 6 years ago
/* End loop at nres-1, since the very last residue does not have a +N atom, and
* therefore we get a valgrind invalid 4 byte read error with atom am */
for(residx=0; residx<nres-1; residx++)
In your case there is only 1 residue, and that's why it fails. I'm not sure what's the proper way to work with that case.