These parameters are partly from Cheatham et al and two entries I have made.
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: Monday, April 17, 2017 11:27 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] HEME-CYS
Thank you so much Dr.Martis
I am using CYM.
Can you let me know from where you have got this parameter?
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Monday, April 17, 2017 6:10:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] HEME-CYS
Hi,
It seems the frcmod you are using has no parameters for FE-S (CYS) or you did not change the residue name from CYS to CYM.
In the former case try adding the following to the corresponding sections in your frcmod file and in the latter case just change the res name to CYM.
BOND
fe-SH 39.00 2.565
ANGLE
SH-fe-nc 48.00 87.595 # average angle
SH-fe-nd 48.00 87.595 # average angle
CT-SH-fe 39.00 105.885
DIHEDRAL
CT-SH-fe-nc 1 0.00 180.000 2.000
CT-SH-fe-nd 1 0.00 180.000 2.000
SH-fe-nd-cd 1 0.00 180.000 2.000
SH-fe-nd-cc 1 0.00 180.000 2.000
cc-nc-fe-SH 1 0.000 180.000 2.000
cd-nd-fe-sh 1 0.000 180.000 2.000
Hope this helps.
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<
http://www.elvismartis.in>
Skype. adrian_elvis12
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Monday, April 17, 2017 10:16 PM
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 - 21:00:03 PDT
