[gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

Gonzalez Fernandez, Cristina cristina.gonzalezfdez at unican.es
Thu Jun 21 14:32:05 CEST 2018

Dear Justin,

Thank you for your suggestion. I have solved the problem!


-----Mensaje original-----
De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] En nombre de Justin Lemkul
Enviado el: jueves, 21 de junio de 2018 1:11
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

On 6/19/18 3:59 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
> I am trying adding Na ions:
> genion -s ions.tpr -o 1lipidA_solv.g96 -p lipidA_gromacsBien.top 
> -pname NA -np 2
> But I get this error:
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file 'lipidA_gromacsBien.top'
> I have check the .top file and I have defined "SOL" in the [ moleculetype ] section before [ molecules ] section:
> [ moleculetype ]
> ; molname       nrexcl
> SOL             3
> [ molecules ]
> ; Compound        #mols
> MOL_1                 1
> SOL                4049
> Also, I have checked the Gromacs manual and other Gromacs users discussion. However, I don´t know how to solve this error, because I think SOL is well defined in the .top file.
> I attach the .top file
> Could anyone help me?

Likely you've got a Windows-style line ending from using a non-plain text editor. Use dos2unix and make sure to only edit files in proper editors like vim, emacs, etc.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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