[gmx-users] RE: no coordinates in .top file

[Owen, Michael]

Fellow gmx users,

thanks for the suggestion, however, applying -v to grompp did not yield any additional information.  Shouldn't grompp read the number of coordinates from the list of atoms in the [ atoms ] section?  Could something be wrong with my .itp file?  Could it be that my .top and .itp files are in my working directory instead of the Gromacs "share" directory?

My .itp file is pasted below:



[ 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 ]

; The force field to be included
#include "ffoplsaa.itp"

	

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


[ system ]


[ molecules ]
; Compound	#mols
TFE		1

Thank you for any suggestions.


Michael Owen





Message: 1
Date: Tue, 10 Oct 2006 00:12:01 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] no coordinates in .top file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <452AC931.2040008 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Owen, Michael wrote:
>
> 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:

Topology looks fine, but grompp =will  give you more info when you run
it with -v. Please read carefully what it saya
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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