[gmx-users] Non Standard residues moving Away

[Souvik Dey]

Hi,

Grompp is running successfully without any errors. But my protein and
ligands are very far away from each other. So, what I fear is that the
interactions among them may not be well accounted for by MD simulations.

On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643