Re: [AMBER] this a very green neophyte's question.

From: Jason Swails <>
Date: Thu, 31 Jul 2014 17:52:28 -0400

On Thu, Jul 31, 2014 at 5:47 PM, J.W. Halley <>

> Warning: detected more than 10 Residue sequence numbers;
> this may be a large multiple residue PDB file;
> large multiple residue PDB files are not supported.
> Continuing, but problems may be encountered.
> Segmentation fault
> Certainly my file contains more than 10 residues. Am I supposed to
> generate a separate pdb file for the RET and CLR residues? I certainly
> don't know how to do that.

​Yes, you are supposed to generate a separate PDB file for RET and another
for CLR and parametrize each of those compounds separately.

Doing so is easy. Open the PDB file up your favorite text editor.​ Copy
the lines containing the atoms in the RET residue and paste them into a new
file. Do the same thing with CLR.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jul 31 2014 - 15:00:04 PDT
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