Dear Sir/Madam,
I am a beginner in MD simulation, and now trying to simulate CYP450 enzymes with CPDI using Amber22.
I have two questions regarding system preparation for the simulation recently.
I have read and followed the parameters for HEM-CPDI and CYP from Shahrok et al, 2012 (
https://doi.org/10.1002/jcc.21922).
However, I'm not sure if it is the best practice for parametrizing CPDI and its attached cysteine(CYP or CYM)
after I found other parameters for heme and CYM residues online.
So, Question1: Is there a need for my preparation to use heme parameters from AMBER parameter database and CYM parameters from ff19SB? Which method is the best way for CPDI parametrization?
Apart from this, I received some disturbing messages when I saved amber parameters of my protein complex in tleap using Shahrok's parameters,
althongh no error reported:
>saveamberparm c complex.prmtop complex.inpcrd
>Building topology
>Building atom parameters
>Building bond parameters
>Building angle parameters,
>Building proper torsion parameters.
>Building improper torsion parameters
> total 1382 improper torsions applied
>Building H-Bond parameters.
>Incorporating Non-Bonded adjustments.
>Not Marking per-residue atom chain types
>Marking per-residue atom chain types.
> (Residues lacking connect0/connect1
> these don't have chain types marked:
> res total affected
> CARG 1
> CYP 1
> HEM 1
> NASN 1
I have used all parameter files including CPDI.frcmod, HEM.mol2, and CYP.mol2 in combine with ff19SB and GAFF, and have connected CYP with two adjacent amino acids and FE using bond comand in tleap.
I wonder why improper torsions applied and CARG, NASN, CYP residues lacked connect0/connect1.
Qustion2: Would these problems lead to improper MD simulation? How could I solve them?
Any suggestions from you would be highly appreciated.
Thanks in advance.
With best regards,
YX. Wang
School of Pharmacy，
Shanghai Jiao Tong University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 15 2024 - 03:30:02 PST
