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
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>> > AMBER mailing list
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>> >
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Received on Wed Jun 28 2017 - 20:30:02 PDT
