i shall try this Andrew Thanks
On Thu, Jun 29, 2017 at 12:16 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> Elvis, I don't think the Heme forcefield parameterized with a Cys ligand
> will work for the His coordinated Heme. If those are the same paramters
> from the Shahrokh paper (
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.21922/epdf). Also, there is
> a great tutorial for Hemes:
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
>
> It's just not listed on the main page of the tutorials. It's under the MCPB
> tutorials, and there is an option to see an example with Heme.
>
> Rana,
>
> Looking at your log file.
>
> > hem = loadmol2 new.mol2
>
> You attempt to load a mol2 of Heme. The problem with this is that your mol2
> file has all tripos atom types, instead of those corresponding to a
> specific forcefield (ex: gaff atom types, ff14sb (parm10.dat) atom types).
>
> Your starting structure of your heme also says a bond length of 1.45004,
> for an Fe-O bond. This is very short. Compound I, has a distance of 1.624
> in the Sharokh paper, and the dioxygen bound species has a Fe-O distance of
> 1.786. If you are going to use this starting structure to feed into MCPB,
> try to give it more realistic bond lengths. I'm assuming you just modeled
> this dioxygen intermediate state manually as there are no crystal
> structures available for it. There is a ton of data available for these
> systems in the literature. If you need a place to start there are a few
> great review papers over in Chem Rev (From ACS), and look at the Shaik
> reviews:
>
> *Theoretical Perspective on the Structure and Mechanism of Cytochrome P450
> Enzymes*
> http://pubs.acs.org/doi/abs/10.1021/cr030722j
>
> *P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by
> QM/MM Calculations*
> http://pubs.acs.org/doi/abs/10.1021/cr900121s
>
>
> Andrew
>
> On Wed, Jun 28, 2017 at 20:28 Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hi Rana,
> >
> > Antechamber doesn't work with metal ions. the frcmod and prepi file I
> sent
> > are ready to be used with your HEME-O2 system. You just need to modify
> your
> > HEME-O2 pdb files to rename the residues name and atom names to match
> that
> > in the frcmod and prepi file.
> >
> > The error you are getting because leap cannot assign the correct
> > parameters because of the mismatch in the atom names or residue name or
> > both.
> >
> >
> > 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: 29 June 2017 01:57:25
> > 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
> >
> > Elvis
> > i used antechamber for my heme fe--o2 ligand it show this error
> >
> > Running: /home/rehan/Downloads/amber16/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > For atom[26]:O01, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > For atom[45]:Fe, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic
> > double)Error: cannot run "/home/rehan/Downloads/amber16/bin/bondtype -j
> > full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> >
> > I have the force field that represent the Heme fe---- O2 and there prep
> > file, in that case how i use the it
> >
> >
> > On Wed, Jun 28, 2017 at 3:18 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> > > 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-wqOl
> > >> XSGjbmEyga9C8lmU1bs-_yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473
> > >> lEq28nSHQ=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.elvismar
> > >> tis.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 - 21:30:04 PDT
