Re: [AMBER] sander minimization file for protein complex

From: Anselm Horn <>
Date: Mon, 09 Apr 2012 14:42:27 +0200

Happy Easter,

> But if I have a protein complex, 1 chain with residue from 1 to 119, the other chain with residue from 1 to 30, will you please tell me the restraintmask?
> If I have a protiein-ligand complex, then how can I define the restraintmask?

Amber has no chain definition, all residues are re-numbered during the
leap-process starting from 1 - a similar issue is often raised for the
correct definition of S-S bonds.

Simply create a top and crd file first, then convert it into a pdb and
have a look at the now unique residue numbers.



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Received on Mon Apr 09 2012 - 06:00:06 PDT
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