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]<
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________________________________
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
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Received on Tue Jun 27 2017 - 23:00:03 PDT
