ok i start it thanks Elvis
On Wed, Jun 28, 2017 at 3:06 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> HI,
>
> Unfortunately, there is no tutorial that uses HEME.
>
> But I understand you have trouble understanding the AMBER workflow when
> non-protein molecules are involved. For this I highly recommend completing
> this tutorial. http://ambermd.org/tutorials/basic/tutorial4b/
>
>
> 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 22:47:39
> 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
>
> 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
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
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> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
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Received on Wed Jun 28 2017 - 12:30:05 PDT
