[gmx-users] CHARMM36 Termini Topology Incomplete

Justin Lemkul jalemkul at vt.edu
Mon May 4 23:47:23 CEST 2015

On 5/4/15 5:43 PM, João Rodrigues wrote:
> Hi Justin,
> In order to solve the issue, I need to know exactly what you're doing -
>> exact
>> command and full pdb2gmx screen output, please.  Issues with missing
>> parameters
>> for neutral termini should have been fixed well over a year ago; you are
>> using
>> the latest ports, correct?  I released a new version last month.  If those
>> files
>> are giving you issues, I need to figure out what's going on.
>> -Justin
> I am using the latest port yes, April 2015, with Gromacs 5.0.4.
> Here's the pastebin for the pdb2gmx command <http://pastebin.com/c2ubYrFg>.
> Here's the pastebin for the grompp command. <http://pastebin.com/J22XMt7N>
> Let me know what I can do to help you debug, or if I'm doing something
> wrong.

I need the topology as well (email off-list if you like) or otherwise a listing 
of the atom types for all of the problematic lines.  This is likely an issue 
specific to a GLY at the N-terminus, triggered only in the case of NH2- as the 
patch, similar to the issue with branched amino acids that we had a while back. 
  It's just impossible to test every combination of every patch and every sequence.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list