[gmx-users] grompp protein-ligand complex simulation
aliyu.adamu.12 at aberdeen.ac.uk
Fri Mar 4 15:03:20 CET 2016
Thanks a lot Justin. I got it right now. What i did was I remove all call directives in the ligand.itp file.
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: Thursday, March 3, 2016 11:04 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] grompp protein-ligand complex simulation
On 3/3/16 12:00 AM, Adamu, Aliyu 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.
There's nothing to do but guess. If you upload all of your input files to a
file-sharing service, we can have a look. But at present, the answer is
"something is screwed up in your topology."
> 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
> Gromacs Users mailing list
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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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