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.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 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
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Jun 27 2017 - 23:30:02 PDT
