RE: AMBER: Problem with antechamber

From: Ross Walker <>
Date: Thu, 2 Aug 2007 08:22:52 -0700

Dear Anju,
Where do you see the word "error" in your text below? What leads you to
conclude that there is an error here? I don't even see the word "warning".


From: [] On Behalf Of
Anju Sharma
Sent: Thursday, August 02, 2007 02:04
Subject: Re: AMBER: Problem with antechamber

Hello Sir,
 Hereby m attaching my frc and prep file along wth Pdb file of drug, Again
quoting my problem below:

While saving topology files and co-ordinate files for drug molecule using
antechamber following error occured:

>saveamberparm MTX /usr/local/try/ /sr/local/try/mtx3.crd
Checking Unit
Building topology
Building atom parameters
Building bond parameters
Building angle parameters
Building proper torsion parameters
Building improper torsion parameters
Old PREP-specified impropers:
<MTX 1>: C16 C1 C17 O18
<MTX 1>: C17 C12 C1 C2
<MTX 1>: C1 C5 C2 O3
<MTX 1>: C7 C2 C5 H6
<MTX 1>: C9 C5 C7 H8
<MTX 1>: C7 C12 C9 O10
<MTX 1>: C13 C9 C12 C1
<MTX 1>: C12 C15 C13 O14
<MTX 1>: C13 C16 C15 C19
<MTX 1>: C17 C15 C16 C42
<MTX 1>: C16 C40 C42 N43
<MTX 1>: C45 C42 N43 H44
<MTX 1>: C42 C38 C40 H41
<MTX 1>: C40 C19 C38 H39
<MTX 1>: C15 C38 C19 N20
<MTX 1>: C22 C19 N20 H21
  total 2 improper torsions applied
  16 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.

Anju Sharma
Project Fellow, 
NIT, Hamirpur (H.P.) 
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Received on Sun Aug 05 2007 - 06:07:34 PDT
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