[gmx-users] gromacs-5.1 with charmm36.ff

Justin Lemkul jalemkul at vt.edu
Fri Sep 11 00:36:34 CEST 2015

On 9/10/15 6:17 PM, Krzysztof Kuczera wrote:
> Hi
> I have run into a strange problem when making an urea+tip3p water box
> When trying to set up an energy minimization with gromacs-5.1  I get a grompp
> error:
> Program gmx grompp, VERSION 5.1
> Source code file:
> /home/kuczera/prog/gromacs-5.1/src/gromacs/gmxpreprocess/toppush.c, line: 908
> Fatal error:
> Unknown bond_atomtype cn9
> Here is the strangeness:
> - grompp and mdrun work OK with version 5.0.4
> - I am using the same force field since winter - from charmm36-nov2014.ff.tar,
> which I add
>     manually to the successive 5.x directories as I upgrade the GROMACS versions
> - my system only has UREA and TIP3P, which do not contain atom names or types = CN9
>     looking in the CHARMM36 merged.rtp file shows that CN9 atoms are in nucleic
> acids

Please get the latest version of the force field from our website.  There have 
been changes related to case sensitivity in the code, and I have updated the 
force field files accordingly.




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