[gmx-users] genion doesn't recognize SOL in top file

[Justin Lemkul]

On 10/17/13 1:01 PM, sunyeping wrote:
> Dear Gromacs users,
> I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8
>
> but it returns a error message saying:
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top'
>
> I checked the topol.top file, but SOL is indeed under [ molecules ] section:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> DRG                 1
> SOL             86574
>
> I know it problem has been disscussed here before, but I cann't fix it out with the avialable information. Could you help me with it?
>

You probably have a non-Unix newline character somewhere.  Run the .top file 
through dos2unix and try again.

-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

==================================================