[AMBER] showing error when creating topology and coordinate file from bharat lakhani on 2009-08-03 (Amber Archive Aug 2009)

From: bharat lakhani <lakhbharat.gmail.com>
Date: Mon, 3 Aug 2009 08:19:59 +0100

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

text/plain attachment: ATT00002.txt

Received on Wed Aug 19 2009 - 20:15:17 PDT