[gmx-users] Non Standard residues moving Away

Mark Abraham mark.j.abraham at gmail.com
Mon Aug 7 19:53:42 CEST 2017


The only thing that matters is the order of the molecules, residues and
atoms, and preferably naming. These must match between topology and
coordinates when you eg use grompp. The point of doing an MD simulation is
generally to keep the topology constant while changing the coordinates. So
give grompp whatever file in whatever format suits you, subject to the
above constraint.


On Mon, 7 Aug 2017 16:25 Souvik Dey <souvik.dey29 at gmail.com> wrote:

> Hi,
> I am trying to simulate a Protein Ligand system. Now, my system has some
> non standard residues and I standardized them for AMBER forcefield using
> ACPYPE. However, when I assemble the gro files of the Proten generated from
> pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
> situated next to each other. They have have moved far away.
> Now, is there any trick by which the coordinates of the PDB file do not
> change while being converted into a gro file or is there any way to restore
> the previous condition of the PDB file?
> Thanking you,
> Souvik Dey
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
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