AMBER Archive (2006)

Subject: AMBER: leap can't assign CALA

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Sep 22 2006 - 17:09:06 CDT

Dear Amber users,

The following is end of my input pdb file.

++++++++++++++++++++++++++++++++++++
ATOM 2996 CG LEU B 390 33.217 -10.365 58.392 1.00 22.89 C
ATOM 2997 CD1 LEU B 390 34.047 -9.969 59.605 1.00 22.56 C
ATOM 2998 CD2 LEU B 390 32.234 -11.469 58.757 1.00 23.11 C
ATOM 2999 N ALA B 391 33.815 -8.670 55.060 1.00 24.14 N
ATOM 3000 CA ALA B 391 34.666 -9.190 53.995 1.00 26.81 C
ATOM 3001 C ALA B 391 35.599 -8.164 53.358 1.00 28.82 C
ATOM 3002 O ALA B 391 36.570 -8.533 52.698 1.00 27.88 O
ATOM 3003 CB ALA B 391 33.800 -9.834 52.916 1.00 26.78 C
ATOM 3004 N ALA B 392 35.311 -6.882 53.557 1.00 29.62 N
ATOM 3005 CA ALA B 392 36.131 -5.822 52.978 1.00 32.31 C
ATOM 3008 CB ALA B 392 35.583 -4.461 53.392 1.00 31.59 C
ATOM 3006 C ALA B 392 37.603 -5.930 53.367 1.00 34.13 C
ATOM 3007 O ALA B 392 37.911 -6.603 54.373 1.00 35.95 O
ATOM 3009 OXT ALA B 392 38.433 -5.316 52.662 1.00 35.48 O
TER
ATOM 3012 FE2 FE2 B 393 20.922 9.956 65.107 1.00 18.17 FE
TER
ATOM 3046 O WAT B 394 22.652 10.270 66.476 1.00 17.36 O
ATOM 3046 H1 WAT B 394 22.583 9.472 67.052 1.00 17.36 O
ATOM 3046 H2 WAT B 394 23.528 10.675 66.602 1.00 17.36 O
TER
END
+++++++++++++++++++++++++++++++++++++++++++++++++

When I look at the log file, leap load all parameters correctly
including terminal map.

However, I've got the following error message.

+++++++++++++++++++++++++++++++++++++++++++++
Created a new atom named: OXT within residue: .R<ALA 392>
One sided connection. Residue: TP3 missing connect0 atom.
  total atoms in file: 1520
  Leap added 1410 missing atoms according to residue templates:
       1410 H / lone pairs
  The file contained 1 atoms not in residue templates
Using Bondi radii
Writing pdb file: pbhbred.pdb
 Converting N-terminal residue name to PDB format: NSER -> SER
Checking Unit.
WARNING: There is a bond of 25.854368 angstroms between:
------- .R<ALA 392>.A<C 9> and .R<FE2 393>.A<FE2 1>
ERROR: The unperturbed charge of the unit: -2.972900 is not integral.
WARNING: The unperturbed charge of the unit: -2.972900 is not zero.
FATAL: Atom .R<ALA 392>.A<OXT 11> does not have a type.
Failed to generate parameters
Parameter file was not saved.
        Quit
++++++++++++++++++++++++++++++++++

Leap can't assign ALA to CALA, and complain missing type of OXT.

Does someone have any idea? 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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