Dear Elvis
Thanks for your guidance. can you suggest me a tutorial for preparing file
for heme containing protein so that i prepare my file before running the
command as you sent me because now i have error that hem.mol2 not present i
have heme in protein system and one more thing my protein have histidine
bond with heme rather then cys
On Wed, Jun 28, 2017 at 2:57 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi Ross, and Rana,
>
> It depends on what file name we keep.
>
> Here is the link for the frcmod for HEME
>
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/
> frcmod.hemall
>
> and the corresponding prepi file
>
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/heme_
> all.in
>
>
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: 28 June 2017 12:20:01
> To: amber.ambermd.org
> Subject: Re: [AMBER] how can i use two force field one is ff14sb other is
> not in leaprc source to produce prmtop and inpcrd files for protein
>
> Maybe it's hem.frcmod?
>
>
>
> On 6/27/17 10:59 PM, Rana Rehan Khalid wrote:
> > loadamberparams frcmod.hem >>>> parameters for HEME (those parameters not
> > defined in gaff)
> >
> > this file is not present sir
> >
> > On Wed, Jun 28, 2017 at 1:36 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> >> Hi,
> >>
> >> Here are the typical commands to be used in leap to prepare your system
> >> for MD
> >>
> >> source leaprc.ff14SB >>> for proteins
> >> source leaprc.gaff >>>> for non-protein ligands including HEME--O2
> system
> >> loadamberparams frcmod.ionsjc_tip3p >>>> parameters for waters and
> >> neutralising ions
> >> loadamberparams frcmod.hem >>>> parameters for HEME (those parameters
> not
> >> defined in gaff)
> >> HEM = loadmol2 hem.mol2 >>>> HEME coordinate file
> >> CYP = loadmol2 cyp.mol2 >>>> CYS (rename this CYS to CYM) residue to
> make
> >> coordinate bond with HEME
> >> 2j2 = loadpdb CYP2J2.pdb >>>> protein system
> >> set 2j2.460.28 element "Fe"
> >> bond 2j2.460.28 2j2.405.8 >>>> making the bond between HEME and CYS
> #BOND
> >> CYS-S to HEM-FE
> >> set 2j2.405 connect0 2j2.405.1
> >> set 2j2.405 connect1 2j2.405.9
> >> bond 2j2.404.9 2j2.405.1 #BOND CYS to the protein (new CYP residue)
> >> bond 2j2.405.9 2j2.406.1 #As above
> >> addions 2j2 Na+ 0
> >> solvateoct 2j2 TIP3PBOX 10
> >> saveamberparm 2j2 CYP2J2_FE_box.prmtop CYP2J2_FE_box.inpcrd
> >>
> >>
> >> Best Regards
> >>
> >> [photo]
> >>
> >>
> >>
> >> Elvis Martis
> >> Ph.D. Student (Computational Chemistry)
> >> at Bombay College of Pharmacy
> >>
> >>
> >> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> >> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> >> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> >>
> >>
> >> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> >> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> >> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> >> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> >> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> >> in/elvisadrianmartis/>
> >>
> >>
> >>
> >>
> >>
> >> ________________________________
> >> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >> Sent: 28 June 2017 10:41:11
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] how can i use two force field one is ff14sb other
> is
> >> not in leaprc source to produce prmtop and inpcrd files for protein
> >>
> >> Yes sir see that but i have the force field .prm for amber heme Fe---O2
> and
> >> i want to know that how i use it with the amber buitin ff to generate
> the
> >> inpcrd and prmtop file
> >>
> >> I paste heme force field into which folder?? so that i can access as we
> >> source some force field like ff14SB it to read my system
> >>
> >>
> >>
> >> On Wed, Jun 28, 2017 at 12:27 AM, Elvis Martis <elvis.martis.bcp.edu.in
> >
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> Please read this post http://archive.ambermd.org/201605/0267.html
> >>>
> >>> Re: [AMBER] How to deal with Heme? from Abelak, Kavin on ...<
> >>> http://archive.ambermd.org/201605/0267.html>
> >>> archive.ambermd.org
> >>> From: Abelak, Kavin Date: Wed, 18 May 2016 12:16:32 +0000 Hi Morteza,
> >> I’ve
> >>> been doing some simulations on CYPs and using HEME parameters from ...
> >>>
> >>>
> >>>
> >>>
> >>> Best Regards
> >>>
> >>> [photo]
> >>>
> >>>
> >>>
> >>> Elvis Martis
> >>> Ph.D. Student (Computational Chemistry)
> >>> at Bombay College of Pharmacy
> >>>
> >>>
> >>> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> >>> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> >>> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> >>>
> >>>
> >>> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> >>> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> >>> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> >>> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> >>> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> >>> in/elvisadrianmartis/>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ________________________________
> >>> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >>> Sent: 28 June 2017 09:24:07
> >>> To: AMBER Mailing List
> >>> Subject: [AMBER] how can i use two force field one is ff14sb other is
> not
> >>> in leaprc source to produce prmtop and inpcrd files for protein
> >>>
> >>> I am working on heme containing protein i have separate force field for
> >>> heme fe---02 how can i use it to prepare initial coordinate file and
> >> prmtop
> >>> file for my heme containing system.
> >>>
> >>>
> >>> Thanks
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
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> >>>
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>
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Received on Wed Jun 28 2017 - 10:30:02 PDT
