AMBER Archive (2005)

Subject: AMBER: D-amino acid prep-files(simple method)

From: Jagdish Rai (jagdish_at_icgeb.res.in)
Date: Sun Jan 23 2005 - 08:18:45 CST

dear sir
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

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