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AMBER Archive (2009)
Subject: [AMBER] showing error when creating topology and coordinate file
From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Mon Aug 03 2009 - 02:19:59 CDT
- Previous message: Bokun Cho: "Re: [AMBER] xleap installation error"
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- Reply: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
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Actually my system having Fe-Porphyrin complex. I performed quantum
calculation in order to make library for (Fe-Porphrin) as directed by the
amber tutorial.But now when i am creating topology and coordinate file for
my system.It showing me following error.Here i am attaching my library with
name *HEM*, *pdb* file.I donot know what to do next if i have to create
frcmod file for my system. Then How i can create frcmod.I think lots of
people right now working on these kind of system.So is there any library
from where i can get frcmod file for my system.Please Help me out.
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.017921 is not integral.
WARNING: The unperturbed charge of the unit: 0.017921 is not zero.
ERROR: The perturbed charge: 0.017921 is not integral.
WARNING: The perturbed charge: 0.017921 is not zero.
-- ignoring the errors and warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C* - CC
Could not find bond parameter for: C* - C*
Could not find bond parameter for: CC - C*
Could not find bond parameter for: C* - CC
Could not find bond parameter for: C* - CD
Could not find bond parameter for: C* - C*
Could not find bond parameter for: CC - C*
Could not find bond parameter for: C* - CC
Could not find bond parameter for: C* - CD
Could not find bond parameter for: C* - C*
Could not find bond parameter for: CC - C*
Could not find bond parameter for: C* - CC
Could not find bond parameter for: C* - C*
Could not find bond parameter for: CC - C*
Building angle parameters.
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: C* - C* - CC
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - NB - CC
Could not find angle parameter: CC - C* - C*
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - C* - CD
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: C* - CD - CM
Could not find angle parameter: C* - CD - HA
Could not find angle parameter: C* - C* - CC
Could not find angle parameter: C* - C* - CD
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - NB - CC
Could not find angle parameter: CC - C* - C*
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - C* - CD
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: C* - CD - HA
Could not find angle parameter: C* - CD - CM
Could not find angle parameter: C* - C* - CC
Could not find angle parameter: C* - C* - CD
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - NB - CC
Could not find angle parameter: CC - C* - C*
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: C* - C* - CC
Could not find angle parameter: C* - C* - CT
Could not find angle parameter: CC - CD - HA
Could not find angle parameter: CC - NB - CC
Could not find angle parameter: CC - C* - C*
Could not find angle parameter: CC - C* - CT
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: NB - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: CD - CC - NB
Could not find angle parameter: CD - CC - C*
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Could not find angle parameter: FE - NB - CC
Building proper torsion parameters.
** No torsion terms for CT-C*-C*-CT
** No torsion terms for CC-C*-C*-CT
** No torsion terms for CC-C*-C*-CC
** No torsion terms for CC-C*-C*-CT
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for CT-C*-C*-CD
** No torsion terms for CC-C*-C*-CT
** No torsion terms for CC-C*-CD-CM
** No torsion terms for CC-C*-CD-HA
** No torsion terms for C*-C*-CD-CM
** No torsion terms for C*-C*-CD-HA
** No torsion terms for CC-C*-C*-CC
** No torsion terms for CC-C*-C*-CD
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CD
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for CT-C*-C*-CD
** No torsion terms for CC-C*-C*-CT
** No torsion terms for CC-C*-CD-HA
** No torsion terms for CC-C*-CD-CM
** No torsion terms for C*-C*-CD-HA
** No torsion terms for C*-C*-CD-CM
** No torsion terms for CC-C*-C*-CC
** No torsion terms for CC-C*-C*-CD
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CD
** No torsion terms for CT-C*-C*-CT
** No torsion terms for CC-C*-C*-CT
** No torsion terms for CC-C*-C*-CC
** No torsion terms for CC-C*-C*-CT
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for NB-CC-C*-C*
** No torsion terms for NB-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CD
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CD
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
** No torsion terms for CD-CC-C*-C*
** No torsion terms for CD-CC-C*-CT
Building improper torsion parameters.
total 12 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
- application/octet-stream attachment: HEM
- chemical/x-pdb attachment: CYP.pdb
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- Previous message: Bokun Cho: "Re: [AMBER] xleap installation error"
- Next in thread: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
- Reply: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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