AMBER Archive (2009)

Subject: RE: [AMBER] Re: showing error when creating topology and coordinate file

• Previous message: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
• In reply to: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
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Hi, I am new to Amber myself but about the library, you can check the link below for supported parameters,if yours is there! good luck

http://www.pharmacy.manchester.ac.uk/bryce/amber

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of bharat lakhani
Sent: Tue 8/4/2009 05:54
To: AMBER Mailing List
Subject: [AMBER] Re: showing error when creating topology and coordinate file
 
Could any one please help me out on this.Yesterday i have asked same
question but did not get any reply.I am stuck here.I am again sending the
same question and expecting that some one take me out to this problem.

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.
>
>
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• Previous message: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
• In reply to: bharat lakhani: "[AMBER] Re: showing error when creating topology and coordinate file"
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