[gmx-developers] Creating topology file

Mansi Porwal mansiporwal2012 at gmail.com
Wed Feb 19 19:14:27 CET 2020

I am using gromacs version 2016.3. I created an ice structure using GenIce Program and used tip5p water model. My output was a .gro file. Now I want to create the topology file of this ice structure. When I am using the command gmx pdb2gmx -f ice5_Ih.gro -o ice5_Ihnew.gro and using charmm36-mar2019 force field I am getting the error “Residue HO5 not found in residue topology database”.  I even tried converting the .gro file I got from GenIce to pdb and then using that pdb for pdb2gmx but it showed the same error. After this I tried making my own topol.top file.
My topol.top file is as follows
;;  The main Gromacs topology file 

; Include forcefield parameters
#include “charmm36-mar2019.ff/forcefield.itp
#include “toppar/tip5p.itp”

; Name

[ molecules ]
; Compound    #mols
Sol                    7943

And then when I am running a gmx grompp command for enery minimization using this topol.top file I am getting the error 
Fatal error:
Syntax error- File tip5-p.itp,  line 6
Last line read:
‘[ moleculetype ]’
Invalid error for directive molecule type.
So can you please tell me what is wrong in my topol.top file or any other method to generate topology file.

Mansi Porwal
M.Sc. Chemistry 

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