[gmx-users] grompp error - no molecules were defined in the system

[Justin Lemkul]

On 1/18/14, 2:20 PM, rankinb wrote:
> When running grompp, I am receiving the error "No molecules were defined in
> the system."  I have a relatively simple topology and .gro file.  I cannot
> locate the source of the error.  Does anyone have any suggestions?  Here is
> an example of the .gro and .top file that I am using.  Thanks.
>
> HSb
>      1
>      1HSb     S2    1   1.250   1.250   1.250
>     2.50000   2.50000   2.50000
>
>
>
>
> [defaults]
> ;nbfunc	comb-rule	gen-pars	fudgeLJ	fudgeQQ
> 1	1	yes	0.5	0.5
>
> [atomtypes]
> ;name	bond_type	mass	charge	ptype	C	A
> HSb		HSb			18.02		0		A	0	0
>
> [nonbond_params]
> ;i	j	func	C	A
> HSb	HSb	1		0	0
>
> [ moleculetype ]
>
> ; Name            nrexcl
>
> HSb              3
>
> [ atoms ]
>
> ;   nr       type          resnr    residue    atom       cgnr   charge
> mass  typeB    chargeB      massB
>           1  HSb         1       HSb        S2 	       1     0   18.02
>
> 		
> [ system ]
> HSb
>
> [ molecules ]
> HSb 1
>

Works fine for me.  Use dos2unix to get rid of any incorrect newline characters 
to see if that's it.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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