AMBER Archive (2006)

Subject: AMBER: how to get complete prepin file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sat Nov 25 2006 - 23:02:20 CST

Dear all,

I have a pdb file as following (See attached):

HEADER Structure from MOLMOL
COMPND CYM_ZN001
ATOM 1 N CYM 33 -2.632 -0.454 0.499
 1.00 0.00
ATOM 2 H CYM 33 -2.424 -0.481 1.487
 1.00 0.00
ATOM 3 CA CYM 33 -1.572 0.022 -0.433
 1.00 0.00
ATOM 4 HA CYM 33 -1.971 0.801 -1.066
 1.00 0.00
ATOM 5 CB CYM 33 -0.391 0.570 0.372
 1.00 0.00
ATOM 6 3HB CYM 33 -0.110 -0.143 1.130
 1.00 0.00
ATOM 7 2HB CYM 33 -0.677 1.500 0.840
 1.00 0.00
ATOM 8 SG CYM 33 1.014 0.862 -0.733
 1.00 0.00
ATOM 9 C CYM 33 -1.104 -1.150 -1.298
 1.00 0.00
ATOM 10 O CYM 33 -0.671 -2.169 -0.798
 1.00 0.00
TER
ATOM 1 Zn Zn 55 2.800 1.527 0.560
 1.00 0.00
TER
END

-------
And I use antechamber and gaussian get the following
prepin file (See attached):

CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0
   .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0
   .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1
   .0 .00000
   4 N1 n2 M 3 2 1 1.540 111.208
180.000 0.00000
   5 H1 hn E 4 3 2 1.006 69.643
108.608 0.00000
   6 C1 c2 M 4 3 2 1.246 45.672
-56.435 0.00000
   7 H2 h4 E 6 4 3 1.079 118.672
-165.213 0.00000
   8 C2 c3 M 6 4 3 1.518 126.013
 14.246 0.00000
   9 H3 h1 E 8 6 4 1.080 111.117
 -5.195 0.00000
  10 H4 h1 E 8 6 4 1.080 109.553
-127.276 0.00000
  11 S1 s M 8 6 4 1.856 106.419
113.919 0.00000
  12 X 1 0 1 1.517 nan
  0.000 0.00000
  13 X 1 0 1 1.517 nan
  0.000 0.00000
  14 X 1 0 1 1.517 nan
  0.000 0.00000

LOOP

IMPROPER
   C2 H2 C1 N1
-----------------------

As we can see, in the prepin file, the last three
atoms was replaced by X, and its parameters are not
complete. When get frcmod file, the frcmod file is
also not complete.

Will you please tell me how can we get the prepin file
so that the prepin file contains the atom type and
charge for all of the atoms in the PDB file?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

 
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