Jon Mujika wrote:
Dear all,
I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:
Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757
However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.
The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.
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
Thanks in advance
Jon
--
========================================
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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