[gmx-developers] Creating topology file
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
[ molecules ]
; Compound #mols
And then when I am running a gmx grompp command for enery minimization using this topol.top file I am getting the 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.
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