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

[Justin Lemkul]

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

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

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