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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>> > > AMBER mailing list
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>> >
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>> > AMBER mailing list
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Received on Wed Jun 28 2017 - 13:30:01 PDT
