AMBER: Problem while creating input files in antechamber

From: Anju Sharma <>
Date: Tue, 31 Jul 2007 11:03:12 +0530

Hello Sir,

While creating input files in antechamber, as directed by you, i encountered
folllowing problem, where i am wrong? Hereby i am attaching Pdb file of the
drug molexcule for your kind consideration.
[root.amber exe]# /usr/local/amber8/exe/antechamber -i
/usr/local/try/mtx2.pdb -fi pdb -o /usr/local/try/mtx2.prepin -fo prepi -c
bcc -s 2

 Unrecognized atomic name M1, exit
 Unrecognized atomic name M2, exit
 Unrecognized atomic name M3, exit
 Unrecognized atomic name 4 M, exit
 Unrecognized atomic name 5 M, exit
 Unrecognized atomic name 6 M, exit

Unrecognized atomic name 56 M, exit
 Unrecognized atomic name 57 M, exit
 Unrecognized atomic name 58 M, exit
 Unrecognized atomic name 59 M, exit

Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o

Total number of electrons: 0; net charge: 0

Running: /usr/local/amber8/exe/divcon
Unable to find mopac charges in divcon.out
 Unrecognized atomic name 60 M, exit[root.amber exe]#

Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Wed Aug 01 2007 - 06:07:30 PDT
Custom Search