AMBER Archive (2002)

Subject: (no subject)

From: deepak rangaswamy (deepak_ramu_at_yahoo.com)
Date: Fri Mar 01 2002 - 05:00:51 CST

Sir

I would like to run minimization for a drug molecule
using AMBER package. When i run leap, it shows the
below detials.
-----------------------

----- Source: ./leap.in
----- Source of ./leap.in done
Loading PDB file: ./trialf.pdb
 (starting new molecule for chain U)
 (starting new molecule for chain V)
 (starting new molecule for chain W)
 (starting new molecule for chain X)
 (starting new molecule for chain R)
 (starting new molecule for chain S)
 (starting new molecule for chain a)
 (starting new molecule for chain b)
 (starting new molecule for chain c)
 (starting new molecule for chain )
Splitting pdb file residue 1 into XXX and G
 1 residues had naming problems.
 Residues split, so res numbers will not correspond to
pdb.
-- residue 1: duplicate NA1 atoms (total 9)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Unknown residue: XXX number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: XXX number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: XXX number: 2 type:
Terminal/beginning
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: T number: 8 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -matched to non-end type residue DT
Unknown residue: A number: 9 type:
Terminal/beginning
..relaxing end constraints to try for a dbase match
  -matched to non-end type residue DA
Unknown residue: C number: 14 type: Terminal/last
..relaxing end constraints to try for a dbase match
 Creating new UNIT for residue: XXX sequence: 0
Created a new atom named: NA1 within residue: .R<XXX
0>
Creating new UNIT for residue: XXX sequence: 1
Created a new atom named: NA1 within residue: .R<XXX
10001>
Creating new UNIT for residue: XXX sequence: 2
Created a new atom named: C1 within residue: .R<XXX
20002>
Created a new atom named: C2 within residue: .R<XXX
20002>
Created a new atom named: C3 within residue: .R<XXX
20002>
Created a new atom named: C4 within residue: .R<XXX
20002>
Created a new atom named: C5 within residue: .R<XXX
20002>
Created a new atom named: C6 within residue: .R<XXX
20002>
Created a new atom named: C7 within residue: .R<XXX
20002>
Created a new atom named: C8 within residue: .R<XXX
20002>
Created a new atom named: C9 within residue: .R<XXX
20002>
Created a new atom named: C10 within residue: .R<XXX
20002>
Created a new atom named: O1 within residue: .R<XXX
20002>
Created a new atom named: O2 within residue: .R<XXX
20002>
Created a new atom named: C11 within residue: .R<XXX
20002>
Created a new atom named: C12 within residue: .R<XXX
20002> -matchCreated a new atom named: C13 within
residue: .R<XXX 20002>
Created a new atom named: C14 within residue: .R<XXX
20002>
Created a new atom named: C15 within residue: .R<XXX
20002>
Created a new atom named: C16 within residue: .R<XXX
20002>
Created a new atom named: C17 within residue: .R<XXX
20002>
Created a new atom named: C18 within residue: .R<XXX
20002>
Created a new atom named: O3 within residue: .R<XXX
20002>
Created a new atom named: C19 within residue: .R<XXX
20002>
Created a new atom named: O4 within residue: .R<XXX
20002>
Created a new atom named: O5 within residue: .R<XXX
20002>
Created a new atom named: C20 within residue: .R<XXX
20002>
Created a new atom named: O6 within residue: .R<XXX
20002>
Created a new atom named: C21 within residue: .R<XXX
20002>
Created a new atom named: O7 within residue: .R<XXX
20002>
Created a new atom named: O8 within residue: .R<XXX
20002>
Created a new atom named: C22 within residue: .R<XXX
20002>
Created a new atom named: O9 within residue: .R<XXX
20002>
Created a new atom named: C23 within residue: .R<XXX
20002>
Created a new atom named: C24 within residue: .R<XXX
20002>
Created a new atom named: C25 within residue: .R<XXX
20002>
Created a new atom named: C26 within residue: .R<XXX
20002>
Created a new atom named: O10 within residue: .R<XXX
20002>
Created a new atom named: C27 within residue: .R<XXX
20002>
Created a new atom named: N1 within residue: .R<XXX
20002>
Created a new atom named: H1 within residue: .R<XXX
20002>
Created a new atom named: H2 within residue: .R<XXX
20002>ed to non-end type residue DC
WARNING: The unperturbed charge of the unit:
-12.000000 is not zero.
FATAL: Atom .R<XXX 0>.A<NA1 1> does not have a type.
FATAL: Atom .R<XXX 10001>.A<NA1 1> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C1 1> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C2 2> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C3 3> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C4 4> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C5 5> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C6 6> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C7 7> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C8 8> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C9 9> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C10 10> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<O1 11> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<O2 12> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C11 13> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C12 14> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C13 15> does not have a
type.
FATAL: Atom .R<XXX 20002>.A<C14 16> does not have a
type.
------------------------------------------------------

>From the error message, what i could guess is AMBER
forcefield is not assigned for this molecule.

sir, can you please tell me how to modify the PDB file
of this molecular.

If i have the charges calculated using GAUSIAN
package, how will i incorporate those charges in the
AMBER library files.

looking forward to your reply.

regards

deepak

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