----- Forwarded message from "Maria khan mariabiochemist1]-[gmail.com" <owner-chemistry.ccl.net> -----
I am running simulation for protein ligand complex that are Glutamate
racemase and its inhibitor KRH.Bt it [gromacs] gives me error like:
" Atom HD1 in residue HIS 61 was not found in rtp entry HISB with 12 atoms
while sorting atoms.For a hydrogen, this can be a different protonation
state, or it might have had a different number in the PDB file and was
rebuilt(it might for instance have been H3, and we only expected H1
& H2).Note that hydrogens might have been added to the entry for the
N-terminus.Remove this hydrogen or choose a different protonation state to
solve it.Option -ignh will ignore all hydrogens in the input."
This might be overdoing it, but seems more user-friendly that what tleap
provides: something like "Creating new atom HD1 in residue 61", with the
actual error, e.g. "missing atom type", coming later in the file.
Would be great if some up-and-coming Amberist could make these common tleap
messages more understandable.
....dac
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Received on Sat Oct 29 2016 - 16:00:02 PDT
