On 8/7/17 3:01 PM, Souvik Dey wrote:
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.
If the coordinates that came out of your topology generation program are
incorrect, then it is pointless to use them. Use the original coordinates from
the bound complex. No sense wasting time with a fruitless simulation when you
already had usable coordinates.
-Justin
On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham <mark.j.abra...@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.de...@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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