[gmx-users] no coordinates in .top file

[Owen, Michael]

Fellow gmx users,

I made a tolopgy file for TFE in water  by "hand" for the OPLSAA/L force field to be used in a simulation containing a mixed solvent.  I made a similar TFE.itp file and included it in the mixed solvent topology file.  when I ran grompp before equilibrating the system I received an error message that read:

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (tfe.gro, 9)
             does not match topology (tfe_mike.top, 0)
-------------------------------------------------------

Do you know why my topology file contains zero coordinates?  My topology file is pasted below:

#include "ffoplsaa.itp"

[ moleculetype ]
; Name 		nrexcl
TFE		3

[ atoms ]
;  nr	type		resnr	residue	atom	cgnr	charge
   1	opls_161	1	TFE	C1	1	 0.797
   2	opls_164	1	TFE	F2	1	-0.285
   3	opls_164	1	TFE	F3	1	-0.280
   4	opls_164	1	TFE	F4	1	-0.278
   5	opls_160	1	TFE	C5	2	-0.033
   6	opls_162	1	TFE	O6	3	-0.479
   7	opls_163	1	TFE	H7	3	 0.292
   8	opls_165	1	TFE	H8	2	 0.133
   9	opls_165	1	TFE	H9	2	 0.132

[ bonds ]
;	ai	aj	funct		c0		c1
	1	2	1 	   0.13570	  351456.0	
	1	3	1	   0.13570	  351456.0	
	1	4	1	   0.13570	  351456.0	
	1	5	1 	   0.15100	  292880.0
	5	6	1	   0.13640	  376560.0
	6	7	1	   0.09450	  462750.4
	5	8	1          0.10900	  284512.0
	5	9	1	   0.10900	  284512.0

[ pairs ]


[ angles ]
;	ai	aj	ak	funct	c0	c1
	2	1	5	1	109.5	418.4		
	3	1	5	1	109.5	418.4
	4	1	5	1	109.5	418.4
	1	5	8	1	110.7	313.8
	1	5	6	1	109.5	418.4
	1	5	9	1	110.7	313.8
	5	6	7	1	108.5	460.24	
	8	5	9	1	107.8	276.144

[ dihedrals ]
;	ai	aj	ak	al	funct	c0	 c1	  c2	   c3	   c4     c5		
	2	1	5	6	3	1.12968  3.38904  0.00000 -4.51872 0.0000 0.0000	 
	3	1	5	6	3	1.12968  3.38904  0.00000 -4.51872 0.0000 0.0000
	4	1	5	6	3 	1.12968  3.38904  0.00000 -4.51872 0.0000 0.0000
	1	5	6	7	3	0.26778	-9.36798  9.10020  0.00000 0.0000 0.0000	
	2	1	5	8	3	0.65689  1.97066  0.00000 -2.62755 0.0000 0.0000
	3	1	5	8	3       0.65689  1.97066  0.00000 -2.62755 0.0000 0.0000
	4	1	5	8	3       0.65689  0.97066  0.00000 -2.62755 0.0000 0.0000
	2	1	5	9	3       0.65689  0.97066  0.00000 -2.62755 0.0000 0.0000
	3	1	5	9	3       0.65689  0.97066  0.00000 -2.62755 0.0000 0.0000
	4	1	5	9	3       0.65689  0.97066  0.00000 -2.62755 0.0000 0.0000
	
[ dihedrals ]

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "tip4p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000	

; Include generic topology for ions
#include "ions.itp"

#include "tfe_mike.itp"

[ system ]
30% TFE in water

[ molecules ]
; Compound	#mols
TFE		14
SOL		128



Thanks in advance for your assistance,

Michael Owen
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