AMBER Archive (2006)

Subject: Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Mon Aug 14 2006 - 11:56:31 CDT

Yes, thank you, I figured out how to do it a couple of minutes ago.

-Amarda

On Mon, 14 Aug 2006, David A. Case wrote:

> On Mon, Aug 14, 2006, Amarda Shehu wrote:
>>
>>
>> I want to construct a short peptide chain, adding peptide bonds as seeing
>> fit. When I try to form a peptide bond between residue x and residue y with
>> the command BOND mol.x.C mol.y.N, I get the following:
>> Building proper torsion parameters.
>> ** No torsion terms for CT-N3-C-CT
>>
>> I am not sure how to suppress amber from adding hydrogens first of all to
>> my initial pdb file, and then how to tell it to add a peptide bond between
>> two arbitrary residues.
>>
>
> By default, Amber makes the first and last residues of a peptide chain
> "terminal" (e.g. with extra hydrogens on the N-terminus.). Change this by
> editing your leaprc file and changing (or removing) the "addPdbResMap"
> section.
>
> It looks like your bond command worked; you just need to make sure that
> residues that should be non-terminal are indeed non-terminal.
>
> ...dac
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