> i need prepfile for all D-amino acid as i am working on
> retroinverso-peptides
> To generate prep file for example D-serine can i edit prep file of
> serine by simply changing the sign of entries in column of 'angle' and
> 'dihedral angle' because there should be no other deffrrence
> D-SERINE
>
> DSE INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
> 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
> 3 DUMM DU M 2 1 0 1.522 -111.100 0.000 0.00000
> 4 N N M 3 2 1 1.335 -116.600 -180.000 -0.41570
> 5 H H E 4 3 2 1.010 -119.800 0.000 0.27190
> 6 CA CT M 4 3 2 1.449 -121.900 -180.000 -0.02490
> 7 HA H1 E 6 4 3 1.090 -109.500 -300.000 0.08430
> 8 CB CT 3 6 4 3 1.525 -111.100 -60.000 0.21170
> 9 HB2 H1 E 8 6 4 1.090 -109.500 -300.000 0.03520
> 10 HB3 H1 E 8 6 4 1.090 -109.500 -60.000 0.03520
> 11 OG OH S 8 6 4 1.430 -109.470 -180.000 -0.65460
> 12 HG HO E 11 8 6 0.960 -109.470 -180.000 0.42750
> 13 C C M 6 4 3 1.522 -111.100 -180.000 0.59730
> 14 O O E 13 6 4 1.229 -120.500 0.000 -0.56790
>
> IMPROPER
> -M CA N H
> CA +M C O
>
> DONE
My understanding is that the AMBER FF libraries can recognized enantiomers and
diastereoisomers. The only thinks important are 'same atom & residues names' in
PDB & OFF libraries. My guess is that you do not need to build your own prep.in
file for these D aminoacids... The RESP charges & atom types are the same for
two enantiomners...
F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
--
http://www.u-picardie.fr/labo/lbpd/FyD.htm
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 23 2005 - 20:53:00 PST
