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

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Thu, 29 Jun 2017 16:33:28 -0400

Ross
I have the .in file and parm file someone work over it before but i do not
know that how i make changes in my PDB file according to pram and prep file
kindly guide how i compare frcmod.in and pram file with pdb

On Thu, Jun 29, 2017 at 4:20 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:

> It turns out that you are modeling a different version of heme, with
> extra O's out of plane.
> This might mean a long learning curve for you, to derive a set of
> charges for this different molecule.
> You should read the tutorials involving parameterizing new residues.
>
> Bill
>
> On 6/29/17 12:05 PM, Rana Rehan Khalid wrote:
> > i search from many places but i do not find that how i compare my hem.pdb
> > with the frcmod.hem and .in leap prototype and there are two residue that
> > are new in hem.pdb which is O01 and O02 the oxygen. i do not know that
> > which part of these files .in and prepi belong to the O2. i saw in the
> .in
> > file have O1A,O2A,O1D and O2D rows show O2 but in my Hem.pdb file the
> same
> > name represent the other part of heme not o2 in the frcmod.hem and .in
> > files here i am attaching my hem file kindly check it
> > thanks
> >
> > On Thu, Jun 29, 2017 at 12:32 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> >> 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
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> >>>>>>>> _______________________________________________
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> >>>>>>>>
> >>>>>>> _______________________________________________
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> >>>>>>>
> >>>>>>
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Received on Thu Jun 29 2017 - 14:00:03 PDT
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