[gmx-users] Adding ion to force field

Justin Lemkul jalemkul at vt.edu
Wed Oct 21 16:38:16 CEST 2015

On 10/21/15 10:25 AM, Peter Stern wrote:
> Just guessing here but maybe you need to also add YB to the atomtypes.atp file.

The .atp file is only read by pdb2gmx, so that's not going to be the issue with 

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Irem Altan
> Sent: Wednesday, October 21, 2015 4:23 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Adding ion to force field
> Thanks, leaving out .ff worked!
> I’m still having a bit of trouble using the resulting .gro and .top files, though. I’m trying to create an executable that adds ions to the box, with the command
> grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
> which gives me the error
> Fatal error:
> Syntax error - File ffnonbonded.itp, line 1 Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> All I did was to add a line to the end of [atomtypes] with the info for the new ion:
> YB          70     173.04    0.0000  A   1.65600e+00  4.00000e-02
> What could be the problem?

So you modified ffnonbonded.itp directly?  grompp is choking on the first line, 
which is really bizarre, so it should have nothing to do with a line added at 
the end.  Can you upload your force field directory somewhere?



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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