[gmx-users] grompp protein-ligand complex simulation

[Christian Bope Domilongo]

maybe try to add "" in your .top file.

; Include generic topology for ions
 #include "oplsaa.ff/ions.itp"


On 3 March 2016 at 13:00, Adamu, Aliyu <aliyu.adamu.12 at aberdeen.ac.uk>
wrote:

> 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.
>
>
> http://www.gromacs.org/Documentation/Errors?highlight=errors#Invalid_order_for_directive_xxx
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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