[gmx-users] RE: Help with simulation

[David van der Spoel]

On Tue, 2003-11-18 at 16:53, Jodi Fangman wrote:
> David thank you for your help, I am now using the OPLS forcefield but once 
> again I am receiving the error message : No moleculetype K+. Do you have any 
> other suggestions?
> Thank you 

replace your ions.itp by the attached file.

> Jodi Fangman
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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#ifdef _FF_GROMACS

[ moleculetype ]
; molname       nrexcl
K               1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr   charge
1       K       1       K               K        1       1

[ moleculetype ]
; molname	nrexcl
Na		1

[ atoms ]
; id	at type	res nr 	residu name	at name	 cg nr	charge
1	Na	1	Na		Na	 1	1

[ moleculetype ]
; molname	nrexcl
Ca		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge
1	Ca	1	Ca		Ca	 1	2

[ moleculetype ]
; molname	nrexcl
Mg		1

[ atoms ]
; id	at type	res nr 	residu name	at name	 cg nr	charge
1	Mg	1	Mg		Mg	 1	2

[ moleculetype ]
; molname	nrexcl
Cl		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge
1	Cl	1	Cl		Cl	 1	-1

[ moleculetype ]
; molname	nrexcl
Zn		1

[ atoms ]
; id	at type	res nr 	residu name	at name	 cg nr	charge
1	Zn	1	Zn		Zn	 1	2

#endif

#ifdef _FF_GROMOS96

[ moleculetype ]
; molname	nrexcl
CU1+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	CU1+	1	CU1+		CU1+	 1	1	 63.54600

[ moleculetype ]
; molname	nrexcl
CU2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	CU2+	1	CU2+		CU	 1	2	 63.54600

[ moleculetype ]
; molname	nrexcl
ZN2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	ZN2+	1	ZN2+		ZN	 1	2	 65.37000

[ moleculetype ]
; molname	nrexcl
MG2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	MG2+	1	MG2+		MG	 1	2	 24.30500

[ moleculetype ]
; molname	nrexcl
CA2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	CA2+	1	CA2+		CA	 1	2	 40.08000

[ moleculetype ]
; molname	nrexcl
NA+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	NA+	1	NA+		NA	 1	1	 22.9898

[ moleculetype ]
; molname	nrexcl
CL-		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	CL-	1	CL-		CL	 1	-1	 35.45300

#endif

#ifdef _FF_OPLS
;
; See literature references in ffoplsaa.itp
;
;[ moleculetype ]
; molname	nrexcl
;CU1+		1

;[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
;1	CU1+	1	CU1+		CU1+	 1	1	 63.54600

[ moleculetype ]
; molname	nrexcl
CU2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	CU2+	1	CU2+		CU	 1	2	 63.54600

[ moleculetype ]
; molname	nrexcl
ZN2+		1

[ atoms ]
; id	at type	res nr 	residu name	at name  cg nr	charge   mass
1	ZN2+	1	ZN2+		ZN	 1	2	 65.37000

[ moleculetype ]
; molname	nrexcl
MG2+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_411	1	MG2+		MG	 1	2	 24.30500

[ moleculetype ]
; molname	nrexcl
CA2+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_412	1	CA2+		CA	 1	2	 40.08000

[ moleculetype ]
; molname	nrexcl
LI+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_406	1	LI+		NA	 1	1	6.941

[ moleculetype ]
; molname	nrexcl
NA+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_407	1	NA+		NA	 1	1	22.98977	 

[ moleculetype ]
; molname	nrexcl
K+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_408	1	K+		K	 1	1	 39.0983

[ moleculetype ]
; molname	nrexcl
Rb+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_409	1	Rb+		Rb	 1	1	85.4678

[ moleculetype ]
; molname	nrexcl
Cs+		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_410	1	Cs+		Cs	 1	1	132.9054

[ moleculetype ]
; molname	nrexcl
F-		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_400	1	F-		F	 1	-1	 18.9984

[ moleculetype ]
; molname	nrexcl
CL-		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_401	1	CL-		CL	 1	-1	 35.45300

[ moleculetype ]
; molname	nrexcl
BR-		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_402	1	BR-		BR	 1	-1	 79.904

[ moleculetype ]
; molname	nrexcl
I-		1

[ atoms ]
; id	at type		res nr 	residu name	at name  cg nr	charge   mass
1	opls_403	1	I-		I	 1	-1	 126.9045

#endif