[gmx-users] CHARMM36 Termini Topology Incomplete

Justin Lemkul jalemkul at vt.edu
Mon May 4 23:28:39 CEST 2015

On 5/4/15 3:43 PM, João Rodrigues wrote:
> Hi all,
> I am trying to setup a simulation of a peptide with neutral termini, using
> the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp
> fails with several erros about missing parameters, e.g.:
> ERROR 1 [file topol.top, line 1225]:
>    No default U-B types
> ...
> ERROR 4 [file topol.top, line 1689]:
>    No default Proper Dih. types
> All these are related to the termini, whether I use CT2 or COOH, or NH2.
> Could I copy the missing parameters from the old CHARMM27.ff files? Or
> should I contact the developers directly? The default charged termini work
> fine.
> Or should I add the ACE/NMA caps in f.e. Pymol?

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 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