[gmx-users] Error : Atomtype not found

Justin Lemkul jalemkul at vt.edu
Thu Jan 8 16:27:44 CET 2015

On 1/8/15 10:14 AM, protim chakraborti wrote:
> Respected Dr. Lemkul
> Thanks for the suggestion. I have checked the ffnonbonded.itp and found
> that copper is entered out there in the following form and format
> ; Ions and noble gases (useful for tutorials)
> Cu2+    29      63.54600        2.00    A       2.08470e-01     4.76976e+00
> Ar      18      39.94800        0.00    A       3.41000e-01     2.74580e-02
> would this be not be suffice or i need to add Cu separately? or may be I
> have to run starting from pdb2gmx itself!

Those parameters are not CHARMM parameters.  They appear to have been copied 
over from OPLS-AA, which had several ions removed due to unknown origins (as was 
Ar).  Do not use these parameters for a CHARMM simulation.  I recommend that 
they be removed entirely, as we did with our CHARMM36 port.



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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