Hi Andrew,
Thanks for correcting, I overlooked that Rana's system was Heme with HIS and not CYS.
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: Andrew Schaub <aschaub.uci.edu>
Sent: 29 June 2017 09:46:13
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 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
> >> > > 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
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Received on Wed Jun 28 2017 - 22:00:04 PDT
