[gmx-users] CMAP error

[Justin A. Lemkul]

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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