[gmx-users] grompp protein-ligand complex simulation

Adamu, Aliyu aliyu.adamu.12 at aberdeen.ac.uk
Thu Mar 3 06:14:29 CET 2016

Thanks Justin for the response. no my protein does not have any Zn2+ bound. as for the alteration of files I only added my ligand topology (dog.itp) in the topology file, also i combined my protein and ligand gromacs coordinate files. this is because i am following  Justin's tutorial for protein-Ligand complex MD simulation but using OPLS-AA forcefield. I check my files very carefully several times, but could not figure out what seems to be wrong. please guid me how to fix this.

many thanks
Aliyu Adamu 
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Tuesday, March 1, 2016 7:21 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] grompp protein-ligand complex simulation

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

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