[gmx-users] Non Standard residues moving Away

Souvik Dey souvik.dey29 at gmail.com
Mon Aug 7 16:25:07 CEST 2017


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
West Bengal

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