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.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
>>> _______________________________________________
>>> 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 - 00:00:04 PDT
