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*
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:17 CST