AMBER Archive (2009)

Subject: [AMBER] Atom type error

From: Vikas Sharma (
Date: Sun Apr 19 2009 - 04:48:01 CDT

Dear All,
I have done molecular docking of a few ligands on a protein...nw i wish to calculate binding free energy of those ligands using MM PBSA
I performed the following steps:
 source leaprc.ff03
 m = loadpdb A.pdb
 saveamberparm m A.prmtop A.inpcrd      then the output was
  warning:The unperturbed charge ofthe unit:9.000000 is not zero
  Fatal: Atom .R<CXL 232>.A<C 1> doesnt have a type
  Fatal: Atom .R<CXL 232>.A<O2 2> doesnt have a type
  Fatal: Atom .R<CXL 232>.A<O1 3> doesnt have a type
  Fatal: Atom .R<AMN 233>.A<N 1> doesnt have a type
Failed to generate parameters

What should i do now??
i performed molecular docking using Sybyl..
i checked in sybyl and got the following information 1. N-terminal configuration (charged=AMN; neutral=AMI).
        2. C-terminal configuration (charged=CXL; netural=CXC).
this means that while protein preparation C-terminal and N-terminal have become charged

Ihave the same protein with ligand on which i have perform the steps as mentioned in the tutorial (like minimizing,heating,equilibrating)

Please helpppppppp....

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