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Joined: Jun 2012
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We don't want any kind of covalent bonds between the receptor and the ligand... We want to study the electrostatic interactions between the ligand and the receptor...


Souparno Adhikary,


Trainee,
Centre of Excellence in Bioinformatics,
Bose Institute,
Kolkata
Joined: Sep 2003
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Then don't include your ligand in the same segment as the protein - split your pdb into two files, one with the protein and one with the ligand. Or create a PRES to delete the unwanted bond.
What you are attempting is a little more advanced than a standard simulation of eg a protein in water, and you should be getting much more support from your supervisor.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Dec 2005
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As for your "amide base" problem with your MTX ligand: that is explained in the FAQ entry linked in my last post.

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