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
>>>>>>>> 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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>>>>> _______________________________________________
>>>>> AMBER mailing list
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>>>>>
>>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>>
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Received on Thu Jun 29 2017 - 13:30:03 PDT
