[gmx-users] CHARMM36 Termini Topology Incomplete

Justin Lemkul jalemkul at vt.edu
Mon May 4 23:30:16 CEST 2015

On 5/4/15 4:09 PM, Jarrett Lee Wise wrote:
> I had similar problems when I was making polymers.  You have to input those
> parameters directly or delete those lines in the itp/topology file depending
> if they are important or not.  The correct way would be to do quantum

I don't know how one decides whether a parameter is "important" or not, but in 
general it's very dangerous to simply make ad hoc deletions.  There should not 
be missing terms, though it is entirely possible that a dihedral will have an 
amplitude of zero (e.g. the normal nonbonded parameters result in a correct 1-D 
energy scan), in which case the deletion is OK.  But this is rare.  Bonds and 
angles should certainly not be deleted because of missing parameters.


> calculations for the missing parameters, but I inserted similar ones for the
> missing ones e.g. CH2 parameter for a CH1 parameter.
> Jarrett Wise
> -----Original Message----- From:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of João
> Rodrigues Sent: Monday, May 04, 2015 1:44 PM To:
> gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] CHARMM36
> Termini Topology Incomplete
> 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?
> Cheers,
> João -- Gromacs Users mailing list
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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


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