[gmx-users] grompp protein-ligand complex simulation

Justin Lemkul jalemkul at vt.edu
Tue Mar 1 19:21:18 CET 2016

On 3/1/16 5:06 AM, Adamu, Aliyu wrote:
> Hi all,
> I am trying to run protein-ligand complex MD in Gromacs 4.6.7. Using opls-aa
> forcefield. I parameterised my ligand using topolbuild. I managed to defined
> the unit cell and added solvent successfully. But when trying to  run grompp
> command for addition of ion, I received fatal error: " atomtype Zn2+ not
> found". I am a kind of confused because my ligand has no any Zn2+ atom. My
> ligand constitutes of only H, O, C, and Cl atoms.

Well, there's no mention of Zn2+ anywhere in the distributed OPLS-AA files, so 
you must have altered something somewhere.  Does your protein have Zn2+ bound? 
Did you alter any other files?  There's ZN2+ in GROMOS and Zn in AMBER, but 
nothing called Zn2+.  Be sure you're not mixing and matching force fields...

> Again, when I included call directive: #include "ff2cp.itp" generated by the
> topolbuild in the ligand topology file (ligand .itp), the error massage
> changed to: Invalid order for directive atomtypes.

Your #include statement is in the wrong place in the topology.




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