AMBER Archive (2003)

Subject: PROBLEM WITH LIBRARY

From: Frederico.Miranda_at_ibmb.uib.no
Date: Thu Jun 05 2003 - 15:06:27 CDT

Hye, I tried to use the following library, made with antechamber:

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    0 0 2
PHOSPHOSERINE

 SEP INT 1
 CORR 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 O1P o M 3 2 1 1.540 111.208 180.000 -0.236
   5 P1 p5 M 4 3 2 1.497 50.096 170.726 1.350
   6 O2P o E 5 4 3 1.487 102.515 -147.525 -0.220
   7 O3P o E 5 4 3 1.479 121.492 92.880 -0.646
   8 OG os M 5 4 3 1.630 107.567 -30.553 -0.545
   9 CB c3 M 8 5 4 1.459 122.177 -165.591 0.219
  10 HB2 h1 E 9 8 5 1.089 106.041 5.526 0.058
  11 HB3 h1 E 9 8 5 1.090 106.030 118.048 0.087
  12 CA c3 M 9 8 5 1.541 112.682 -118.236 -0.087
  13 N n4 M 12 9 8 1.454 114.481 -112.250 -0.760
  14 HA hx E 12 9 8 1.090 107.617 8.108 0.150
  15 C c M 12 9 8 1.532 113.304 126.199 0.889
  16 O o M 15 12 9 1.225 121.282 54.401 -0.575

IMPROPER
 -M CA N H
 CA +M C O

DONE
STOP

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but I got this message, when I used it in leap:

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FATAL: Atom .R<SEP 16>.A<OG 1> does not have a type.
FATAL: Atom .R<SEP 16>.A<CB 2> does not have a type.
FATAL: Atom .R<SEP 16>.A<HB3 3> does not have a type.
FATAL: Atom .R<SEP 16>.A<HB2 4> does not have a type.
FATAL: Atom .R<SEP 16>.A<N 5> does not have a type.
FATAL: Atom .R<SEP 16>.A<H 6> does not have a type.
FATAL: Atom .R<SEP 16>.A<CA 7> does not have a type.
FATAL: Atom .R<SEP 16>.A<HA 8> does not have a type.
FATAL: Atom .R<SEP 16>.A<C 9> does not have a type.
FATAL: Atom .R<SEP 16>.A<O 10> does not have a type.
FATAL: Atom .R<SEP 16>.A<P1 11> does not have a type.
FATAL: Atom .R<SEP 16>.A<O1P 12> does not have a type.
FATAL: Atom .R<SEP 16>.A<O2P 13> does not have a type.
FATAL: Atom .R<SEP 16>.A<O3P 14> does not have a type.
Failed to generate parameters
Parameter file was not saved.

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my input file was:

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source leaprc.ff99
loadAmberPrep SEP.lib
PO4 = LoadPDB WTPO4.pdb
saveAmberParm PO4 WTPO4.prmtop WTPO4.inpcrd
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could somebody help me please?

Thank you,

Frederico Miranda