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
