AMBER Archive (2009)

Subject: [AMBER] Parameter file not saved

From: Remya S R (amm07bi022_at_students.amrita.ac.in)
Date: Mon May 04 2009 - 01:30:19 CDT

Dear Amber users,
                     I was trying to simulate a complex of dna with Furamidine. I used tlep to create input files for sander. But it generated an error as follows.I can't figure out the error. Please help me. It is very urgent.

 Added missing heavy atom: .R<BGF 25>.A<N2' 23>
  Added missing heavy atom: .R<BGF 25>.A<C7' 21>
  Added missing heavy atom: .R<BGF 25>.A<N1' 22>
  Added missing heavy atom: .R<BGF 25>.A<C6' 20>
  Added missing heavy atom: .R<BGF 25>.A<CB' 3>
  Added missing heavy atom: .R<BGF 25>.A<CA' 4>
  total atoms in file: 801
  Leap added 12 missing atoms according to residue templates:
       6 Heavy
       6 H / lone pairs
  The file contained 12 atoms not in residue templates
  Since added/missing = extra, there is a high probability
  of atoms with 'incorrect' names; you may want to
  use addPdbAtomMap to map these names, or change in file
Checking Unit.
WARNING: The unperturbed charge of the unit: -24.000300 is not zero.
FATAL: Atom .R<BGF 25>.A<CB* 42> does not have a type.
FATAL: Atom .R<BGF 25>.A<CA* 43> does not have a type.
FATAL: Atom .R<BGF 25>.A<C6* 44> does not have a type.
FATAL: Atom .R<BGF 25>.A<C7* 45> does not have a type.
FATAL: Atom .R<BGF 25>.A<N1* 46> does not have a type.
FATAL: Atom .R<BGF 25>.A<N2* 47> does not have a type.
FATAL: Atom .R<BGF 25>.A<HB* 48> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2* 49> does not have a type.
FATAL: Atom .R<BGF 25>.A<H5* 50> does not have a type.
FATAL: Atom .R<BGF 25>.A<H6* 51> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1*1 52> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1*2 53> does not have a type.
Failed to generate parameters
Parameter file was not saved.
        Quit

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