AMBER Archive (2009)

Subject: Re: [AMBER] Load protein complex to Xleap (Combine)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Mar 28 2009 - 21:26:58 CDT

On Sun, Mar 29, 2009, Rilei Yu wrote:

> I ever came across a problem-when I docked small peptideswith anmino
> acid residues aranged between 12_20. You know, when I docked them in to
> the protein in sybyl, I found these peptides were not considered to be
> usual amino acid any more. So I have to load those small peptide in the
> mol2 form.

I'm lost here: when you say "load those small peptide", do you mean into
Sybyl? For Amber, it would certainly be easier to use the loadpdb
command, and use the same force fields as we usually use for proteins.
If all you have are amino acids, there should be no reason to use
antehcamber at all.

...dac

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