[gmx-users] Protein ligand simulation topology

[Justin Lemkul]

On 10/8/19 7:30 AM, DEEPANSHU SINGLA wrote:
> Respected sir/mam,
>
> While doing the simulation of my protein with a ligand I received the
> following error:
>
> Fatal Error:
> No line with moleculetype 'SOL' found in the [molecules] section of the
> 'topol.top'
>
> Molecule section of my topology file is as follows:
>   [molecules]
> ; Compound        #mols
> Protein_chain_A     1
> AB1                         1
> SOL                 17416
>
> Also the number of SOL molecules in the topology file do not match with the
> ones shown in the terminal for selecting the continous group of solvent. In
> the terminal number of solvent molecules is 52248.
>
> Please help me resolve this issue.

You probably have Windows-style line endings. Use dos2unix to fix the 
.top file and be sure to always use a plain-text editor.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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