[gmx-users] genion doesn't recognize SOL in top file
jalemkul at vt.edu
Thu Oct 17 19:28:09 CEST 2013
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 A. Lemkul, Ph.D.
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
More information about the gromacs.org_gmx-users