Jon Mujika wrote:
Dear Justin,
Thanks for your advice. You were wright. The problem was solved adding
the new residue name to residuetypes.dat
The issue was that when pdb2gmx found an unknown residue name, it
defined as "Others" system instead of "Protein". As a consequence,
the chain was capped there, adding a COO- termination to the "last"
residue of the protein.
Thanks again for the fast and efficient answer.
Bugzilla 621 filed. Thanks for discovering this.
http://bugzilla.gromacs.org/show_bug.cgi?id=621
-Justin
Jon
I can't promise a solution, but you could try adding LSN and whatever other
non-standard residues you need to use in residuetypes.dat. I noticed that LSN
is not there, which seems like an omission, since the other CHARMM-specific
residue names are there. When LYS is present, probably pdb2gmx is correctly
interpreting the residue as protein before converting its name. In the case of
LSN or any other non-standard residue, this may not be the case. Check the
output of pdb2gmx carefully for any messages that might indicate that a residue
of type "Other" was detected. I've had this cause other problems.
If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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