[gmx-users] Adding ion to force field

[Justin Lemkul]

On 10/21/15 11:59 AM, Irem Altan wrote:
> 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 )
>

You've screwed up forcefield.itp:

;[ defaults ]
  nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ

needs to be

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ

So everything gets totally misinterpreted, since [ defaults ] has to be the 
first directive read.  In your case, [ atomtypes ] is the first directive and 
you get a fatal error.

-Justin

> Irem
>
>
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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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
http://mackerell.umaryland.edu/~jalemkul

==================================================