Re: [AMBER] HEME-CYS

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Tue, 18 Apr 2017 03:30:25 +0000

Hi,
Please only append the values I send without replacing the older entries.
Please share the relevant coordinate file so that we can have a closer look at it.

    Best Regards



Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy


A  Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12




-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Tuesday, April 18, 2017 12:08 AM
To: amber.ambermd.org
Subject: Re: [AMBER] HEME-CYS

Hi Dr.Martis

After using your values I have tried to make parameter file for my complex but slill some values seems to be missing


Could not find bond parameter for: CY - CX Could not find bond parameter for: CY - CX Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HEM 527>: NA C1A C4A FE
 <HEM 527>: NB C1B C4B FE
 <HEM 527>: NC C1C C4C FE
 <HEM 527>: ND C1D C4D FE
 <HEM 527>: C1A C2A NA CHA
 <HEM 527>: C1B C2B NB CHB
 <HEM 527>: C1C C2C NC CHC
 <HEM 527>: C1D C2D ND CHD
 <HEM 527>: C2A C3A C1A CAA
 <HEM 527>: C2B C3B C1B CMB
 <HEM 527>: C2C C3C C1C CMC
 <HEM 527>: C2D C3D C1D CMD
 <HEM 527>: C3A C4A C2A CMA
 <HEM 527>: C3B C4B C2B CAB
 <HEM 527>: C3C C4C C2C CAC
 <HEM 527>: C3D C4D C2D CAD
 <HEM 527>: C4A NA C3A CHB
 <HEM 527>: C4B NB C3B CHC
 <HEM 527>: C4C NC C3C CHD
 <HEM 527>: C4D ND C3D CHA





________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: Monday, April 17, 2017 5:45:38 AM
To: amber.ambermd.org
Subject: [AMBER] HEME-CYS

Hi

I am having a system in which HEME FE is bounded to Cys S.

When I am using HEME amber parameters and manually giving bond between FE and S, I am getting an error



Could not find bond parameter for: SH - FE Building angle parameters.
Could not find angle parameter: SH - FE - NP Could not find angle parameter: SH - FE - NO Could not find angle parameter: SH - FE - NP Could not find angle parameter: SH - FE - NO Could not find angle parameter: CT - SH - FE Building proper torsion parameters.
 ** No torsion terms for CT-SH-FE-NP
 ** No torsion terms for CT-SH-FE-NO
 ** No torsion terms for CT-SH-FE-NP
 ** No torsion terms for CT-SH-FE-NO


How should I solve this problem.




with regards,

-AT
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Received on Mon Apr 17 2017 - 21:00:02 PDT
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