Re: Difficulties is minimizing capped peptides

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Mar 06 2007 - 00:19:08 CST

Hi Kate,

Have you tried with CT3 instead of CT2? I don't know whether this makes a
difference but I always use CT3 when capping the C-terminus.

Gianluca

On Tue, 6 Mar 2007, kate.nairn_at_csiro.au wrote:

> Hi,
>
> I am attempting to simulate 10-residue peptides in explicit water with
> salt. I can perform minimization, equilibration and dynamics runs on
> peptides without caps. But when I try to carry out similar processes on
> peptides with capped termini, things get strange.
>
>
>
> The caps are applied using the following patch residues in PSFGEN:
> N-terminal ACE and C-terminal CT2
>
>
>
> The initial pdb/psf files look fine. The problems arise early on in the
> minimization process, where both the methyl group in the ACE cap and the
> NH2 group of the CT2 cap turn "inside out", with the hydrogen atoms all
> pointing back towards the main chain. Eventually the total energy does
> go to a minimum, the gradient tolerance decreases to around 4 after
> 1000 steps, but these "inside-out" groups remain.
>
>
>
> Any attempt to subsequently equilibrate these structures results in
> "constraint failure in rattle algorithm" early in the equilibration
> (either in the 0-25K step or 25-50K step).
>
>
>
> Other than manually pulling the atoms back closer to where they should
> be, or not minimizing the structure in the first place, are there any
> ways of making ACE and CT2 caps behave better?
>
>
>
> Thanks in advance
>
> Kate
>
>
>
> Kate Nairn
>
> Research Scientist - Biopolymer Characterisation
>
> CSIRO Manufacturing and Materials Technology
>
> Gate 5, Normanby Rd, Clayton, 3168
>
>
>
> phone :+61 3 9545 2667
>
> fax: +61 3 9544 1128
>
>
>
>
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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