Dear all,
i am trying to a do a simulation of a reduced cytochrome c protein [pdbid:
2GIW], using Amber forcefield (amber99sb) .
using the RESP charges provided in the paper by Prof.Zaida Luthey-Schulten
(
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20079/pdf), i have created
the lib files for 2 cysteines (CYM), 1 histidines(HIC), 1 methionine(MEM)
and HEM moeity and tried to prepare the frcmod and prepin files.
but, i am getting the following error while creating the frcmod files for
the molecule :
building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: SH - CY - CB
Could not find angle parameter: SH - CY - HC
Could not find angle parameter: SH - CY - CX
Could not find angle parameter: CT - SH - CY
Could not find angle parameter: SH - CY - CB
Could not find angle parameter: SH - CY - HC
Could not find angle parameter: SH - CY - CX
Could not find angle parameter: CT - SH - CY
Could not find angle parameter: NB - FE - S
Building proper torsion parameters.
** No torsion terms for CT-SH-CY-CB
** No torsion terms for CT-SH-CY-HC
** No torsion terms for CT-SH-CY-CX
** No torsion terms for CT-SH-CY-CB
** No torsion terms for CT-SH-CY-HC
** No torsion terms for CT-SH-CY-CX
** No torsion terms for NB-FE-S-CT
** No torsion terms for NB-FE-S-CT
** No torsion terms for CT-S-FE-NP
** No torsion terms for CT-S-FE-NO
** No torsion terms for CT-S-FE-NP
** No torsion terms for CT-S-FE-NO
** No torsion terms for CT-S-FE-NP
** No torsion terms for CT-S-FE-NO
** No torsion terms for CT-S-FE-NP
** No torsion terms for CT-S-FE-NO
Is it appropriate to us the parmaters provided in the Charmm paramater
files ..?
Can anybody please provide the frcmod and prepin files or suggest me how to
go about ..?
Thank you
Gurunath
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Received on Thu Mar 22 2012 - 20:00:03 PDT
