AMBER Archive (2009)
Subject: [AMBER] Atom type error
From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sun Apr 19 2009 - 04:48:01 CDT
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:
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)
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