BTW, there is an easy option to make cmd.fab() to pick the fragments from an alternative location? (just to avoid modifying the original fragments files)



On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin <> wrote:
Ok, I will try editing those files.



On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees <> wrote:
Hi Osvaldo,

This isn't built in yet. But, if you need to do that, you can edit the
Python picked files found here:



-- Jason

On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin <> wrote:
> I am using the comand cmd.fab() to create small peptides. There is an easy
> option to add neutral aminoacids? The default behaviour is to add charged
> amino acids with the charge of the free amino acid in solution at pH = 7
> i.e. Lys and Arg protonated and Glu, Asp and His unprotonated.
> Thanks in advance.
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Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(o) +1 (603) 374-7120