HI
i am sending you the leap log kindly guide me where i am wrong
On Wed, Jun 28, 2017 at 4:27 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> 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-wqOlXSGj
>>> bmEyga9C8lmU1bs-_yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq2
>>> 8nSHQ=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/am
>>> ber/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.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 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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 28 2017 - 16:00:02 PDT
