[gmx-users] Adding ion to force field

Irem Altan irem.altan at duke.edu
Wed Oct 21 18:00:03 CEST 2015

I have uploaded the zipped folder here: http://iremaltan.com/amber99sb.ff.tar.gz
(Or if you would like the see the specific file, http://iremaltan.com/ffnonbonded.itp )


On Oct 21, 2015, at 10:38 AM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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 grompp.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto: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<mailto: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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441

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