[gmx-users] Adding ion to force field

[Peter Stern]

Just guessing here but maybe you need to also add YB to the atomtypes.atp file.

-----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?

Best,
Irem

On Oct 21, 2015, at 2:03 AM, Peter Stern <peter.stern at weizmann.ac.il<mailto:peter.stern at weizmann.ac.il>> wrote:

Or leave out the .ff:
pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -o box.gro -p topol.top

Peter

-----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 Justin Lemkul
Sent: Wednesday, October 21, 2015 4:50 AM
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] Adding ion to force field



On 10/20/15 7:19 PM, Irem Altan wrote:
Hi,

I am trying to add an ion to amber99sb.ff. For this, I copied the amber99sb.ff folder to the folder I’m working in, and I also copied residuetypes.dat into the same directory. However, when I do pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb.ff -o box.gro -p topol.top, I get an error saying Could not find force field 'amber99sb.ff' in current directory, install tree or GMXDATA path.

Try selecting interactively, not using -ff.

-Justin

I am using GROMACS 4.6.5. My working folder looks something like:

1ytt_refine_001.pdb  nvt.mdp                               residuetypes.dat           topol.top
amber99sb.ff         posre_Protein_chain_A.itp             topol_Protein_chain_A.itp  posre_Protein_chain_B.itp  topol_Protein_chain_B.itp

and the contents of amber99sb.ff  are:

aminoacids.arn    aminoacids.r2b  dna.arn  ffbonded.itp     gbsa.itp  rna.r2b   tip3p.itp    urea.itp
aminoacids.c.tdb  aminoacids.rtp  dna.hdb  ffnonbonded.itp  ions.itp  rna.rtp   tip4pew.itp  watermodels.dat
aminoacids.hdb    aminoacids.vsd  dna.r2b  forcefield.doc   rna.arn   spce.itp  tip4p.itp
aminoacids.n.tdb  atomtypes.atp   dna.rtp  forcefield.itp   rna.hdb   spc.itp   tip5p.itp

I only modified ffbonded.itp ions.itp atomtypes.atp  within the force field folder, and also residuetypes.dat in the working folder. What could be the problem?

Best,
Irem


--
==================================================

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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