[gmx-developers] Creating topology file

[Berk Hess]

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Cheers,

Berk

On 2020-02-19 19:08, Mansi Porwal wrote:
>
> 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”
>
> [system]
>
> ; Name
>
> Icebox
>
> [ 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.
>
> Regards,
>
> Mansi Porwal
>
> M.Sc. Chemistry
>
>

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