From: Aaron Oakley (oakley_at_rsc.anu.edu.au)
Date: Tue Oct 26 2004 - 03:05:28 CDT
Its fairly easy to convert the standard topologies
for the regular L-amino acids to D-aminoacids:
In the topology file, convert
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
to:
IC N C *CA CB 1.4592 114.4400 -123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 120.4500 106.3900 1.0840
This will allow the main-chain HA to be built correctly in PSFGEN
...This is assuming that the coordinates have already been built
as D-amino acids.
aaron++
On 25/10/2004, at 10:00 PM, Giovanni Bellesia wrote:
> Hi,
> I need to start a trial run of a short peptide built with D-amino
> acids.
> Has anybody any experience in that ?
> Anybody knows how to find detailed information about parameter files ?
> Thanx
>
> Giovanni
>
>
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