Re: CHARMM FF parameters for FE-S bond in CYP450

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Wed Jul 18 2018 - 11:20:37 CDT

I attach here the psfgen details. The patch was applied to Cys442 and
HEME504 bond.

Thank you.

Jeevan

----------------------------------
package require psfgen

topology top_all36_prot.rtf
topology toppar_all36_prot_heme_hem.str

pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias atom HOH O OH2
pdbalias residue HOH TIP3

segment P {pdb protein.pdb}
coordpdb protein.pdb P
regenerate angles dihedrals
segment H {pdb hem.pdb}
coordpdb hem.pdb H
patch PSUL P:442 H:504
guesscoord
writepdb protein_heme.pdb
writepsf protein_heme.psf
exit

-------------------------------------

On Tue, Jul 17, 2018 at 4:43 PM jeevan gc <gcjeevanbdr_at_gmail.com> wrote:

> Thank you. I could solved the issue using your suggestions.
>
> On Tue, Jul 17, 2018 at 2:54 PM JC Gumbart <gumbart_at_physics.gatech.edu>
> wrote:
>
>> There appear to be parameters in the same file that you found the PSUL
>> patch - toppar_all36_prot_heme.str.
>>
>> Best,
>> JC
>>
>> > On Jul 17, 2018, at 5:39 PM, jeevan gc <gcjeevanbdr_at_gmail.com> wrote:
>> >
>> > Dear all,
>> >
>> > I am trying to setup CYP450 MD simulation system. I applied a patch
>> PSUL to define a coordination between amino acid residues CYS and FE atoms
>> of HEME. The created psf and pdb files of the system has a bond between
>> CYS:S-FE: HEME as visualized in VMD.
>> >
>> > Could you please refer a published articles or any references that
>> includes CHARMM36 bond angle dihedrals parameter for this coordination?
>> >
>> > Thank you.
>> >
>> > Jeevan
>> >
>>
>>
>
> --
> *Jeevan B. GC, Ph.D*
> *Post Doctoral Research Associate*
> *Department of Pharmaceutical Sciences*
> *Washington State University*
> *Spokane, WA 99224 , **USA*
>

-- 
*Jeevan B. GC, Ph.D*
*Post Doctoral Research Associate*
*Department of Pharmaceutical Sciences*
*Washington State University*
*Spokane, WA 99224 , **USA*

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