[gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Wed Jan 23 16:35:25 CET 2019


Hi
Gromacs is saying that the BCD residue is not present in gromacs list. You
have to create topology for that residue.

On Wed 23 Jan, 2019, 6:39 PM Edjan Silva <edjan.silva at esenfar.ufal.br wrote:

> I can not generate topologies for a medium molecule
> (beta-cyclodextrin) using the "gmx pdb2gmx". I've tested all the force
> fields.
>
> how to generate the topology files for beta-cyclodextrin using gmx?
>
>
>
> ---------------------------------------------------------------------------------------
>
> Program:     gmx pdb2gmx, version 2019-beta3
> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 618)
>
> Fatal error:
> Residue 'BCD' not found in residue topology database
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