Hello Vaibhav,
I understand your confusion. The good news is that if you have the non-standard residue force field setup and the charges for all redox states computed, then you are almost done.
Your next step is to add the definitions for your new residue into $AMBERHOME/AmberTools/src/parmed/parmed/amber/titratable_residues.py . I suggest you to "copy and paste" the definitions for the HEH residue and start from that. The only information you will not have when editing this file are the reference energies (but that is fine, because you will get these later with finddgref.py). Initially you should just place random reference energy values in the titratable_residues.py file (or simply keep the values for the HEH there). Once you complete editing titratable_residues.py, you should recompile AmberTools. Then you will be able to use ceinutil.py to generate a CEIN file (with the wrong reference energies) for your reference system. With this CEIN file you will be able to use finddgref.py to find the reference energies. Once finddgref.py completes, you just need to update the correct reference energy values into titratable_residues.py and recompile AmberTools again. More information about what I am describing (and about how to use finddgref.py) can be found at the section 22.5 of the Amber18 manual.
I hope this helps,
Please let me know if you have any questions further,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Sent: Thursday, May 30, 2019 10:38 AM
To: AMBER Mailing List
Cc: Cruzeiro,Vinicius Wilian D; Roitberg,Adrian E; marcossamaral.gmail.com
Subject: Re: [AMBER] empty cein file redox potential calculations
Dear All,
I'm slightly confused about the usage for ceinutil.py and finddgref.py programs.
ceinutil.py can't generate cein for non-standard residues and finddgref.py also requires cein file.
My question is how do I generate the cein file for non-standard residues assuming I have charges for oxd/red states from literature or G09 jobs.
Thanks in advance.
regards
On Thu, May 30, 2019 at 1:39 PM Marcos Serrou do Amaral <marcossamaral.gmail.com<mailto:marcossamaral.gmail.com>> wrote:
Dear Dr. Vaibhav,
>Does that mean that I will have to run the finddgref.py program and follow
>instructions in the Amber18/19 manual (note copied below from tutorial)?
Yes.
I have used finddgref.py instead of TI calculations.
>Does it require one or two electron redox states or it can handle any?
You need to have both redox states charges.
>Which one was used in the tutorial?
finddgref.py with two redox states.
Best Regards
---
Marcos S.A.
On Thu, May 30, 2019 at 8:17 AM Vaibhav Dixit <vaibhavadixit.gmail.com<mailto:vaibhavadixit.gmail.com>>
wrote:
> Dear Macros S.A.
> Does that mean that I will have to run the finddgref.py program and follow
> instructions in the Amber18/19 manual (note copied below from tutorial)?
> Does it require one or two electron redox states or it can handle any?
> Which one was used in the tutorial?
> Thanks for the clarification and quick response.
> best regards
>
> *Note:* if you want to run simulations for redox-active residues that are
> not yet parametrized, please check the section *Extending constant Redox
> Potential to additional titratable groups* in the Amber manual
> <http://ambermd.org/Manuals.php<https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_Manuals.php&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=6nuKpsZBI7w_KlDSB8gUanIYhVuUYT-Dfi6-cfvIyzo&s=nqeR8GNt_1KqxlmehJ4Wnkd12ChMhssoqrs9arjlWds&e=>>. The *finddgref.py* AmberTool or TI
> calculations can be used to compute the necessary reference energies of
> each redox state.
>
> On Thu, May 30, 2019 at 1:04 PM Marcos Serrou do Amaral <
> marcossamaral.gmail.com<mailto:marcossamaral.gmail.com>> wrote:
>
> > Dear Dr. Vaibhav,
> >
> > The only HEME residue implemented in Ambertools is the bis-HIS Heme
> (HEH).
> > For CYP450, you need the CYS-HEME, right?
> > So, you need to find in the literature for CYS-HEME charges (oxidized and
> > reduced states) and implement these residues to have C(pH,E)-MD
> simulation
> > for CYP450.
> >
> > Best Regards,
> > ---
> > Marcos S.A.
> >
> >
> >
> > On Thu, May 30, 2019 at 7:37 AM Vaibhav Dixit <vaibhavadixit.gmail.com<mailto:vaibhavadixit.gmail.com>>
> > wrote:
> >
> > > Dear AMBER and ConspH/Redox tool experts
> > > I have prepared a CYP450 system with details similar to those here
> > > <http://archive.ambermd.org/201504/0120.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201504_0120.html&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=6nuKpsZBI7w_KlDSB8gUanIYhVuUYT-Dfi6-cfvIyzo&s=93i5u3wuxME3rzqLH7eIW7L26-cvk_m1uKllG_f4Ozg&e=>>.
> > > While generating the cein file I'm getting a file (shown below) with no
> > > charge/redox information.
> > > The corresponding tutorial (with different HEM) file shows charge info
> > here
> > > <http://ambermd.org/tutorials/advanced/tutorial33/files/mp8_is.cein<https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial33_files_mp8-5Fis.cein&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=6nuKpsZBI7w_KlDSB8gUanIYhVuUYT-Dfi6-cfvIyzo&s=e7TaORuuYCL1MnBYUlwMAHp4uGn_M4-GwjwsNulvqMU&e=>>.
> > > A similar command for the cpin file gives meaningful output (shown
> > below).
> > > (My latest post on Amber on this system is not archived yet title:
> error
> > > with loading HEM parameters for constph redox calculations)
> > > Can you please suggest where is the error most likely to be; in my
> prmtop
> > > (it has info on HEH residue) or something else?
> > > thanks a lot.
> > > PS (Dr. Roitberg, sorry if you got a duplicate copy of this email, my
> > > attachment was blocked by Amber mailing list, thus resubmitting to list
> > > without prmtop file).
> > >
> > > The command used for cein file.
> > > [r11831vd.hlogin2 [csf3] 3A4]$ ceinutil.py -resnames HEH -p
> > > P450-1W0E-gas2.prmtop -igb 2 -o P450-1W0E-gas.cein
> > > CEIN generation complete!
> > > [r11831vd.hlogin2 [csf3] 3A4]$ more P450-1W0E-gas.cein
> > > &CNSTE
> > > CHRGDAT=
> > > ELECCNT=
> > > RESNAME='System: Unknown',
> > > RESSTATE=
> > >
> > > STATENE=
> > > EO_CORR=
> > > TRESCNT=0,
> > > /
> > > [r11831vd.hlogin2 [csf3] 3A4]$ grep HEH P450-1W0E-gas2.prmtop
> > > HEH GLY THR HIE SER HIE GLY LEU PHE LYS LYS LEU GLY ILE PRO GLY PRO THR
> > PRO
> > > LEU
> > >
> > > The command used for cpin file
> > > -----------------
> > > [r11831vd.hlogin2 [csf3] 3A4]$ cpinutil.py -resnames PRN TYR GL4 AS4
> -p
> > > P450-1W0E-gas2.prmtop -igb 2 -o P450-1W0E-gas.cpin
> > > CPIN generation complete!
> > > [r11831vd.hlogin2 [csf3] 3A4]$ more P450-1W0E-gas.cpin
> > > &CNSTPH
> > >
> > >
> >
> CHRGDAT=-0.4157,0.2719,-0.0014,0.0876,-0.0152,0.0295,0.0295,-0.0011,-0.1906,
> > >
> >
> 0.1699,-0.2341,0.1656,0.3226,-0.5579,0.3992,-0.2341,0.1656,-0.1906,0.1699,
> > >
> > >
> >
> 0.5973,-0.5679,-0.4157,0.2719,-0.0014,0.0876,-0.0858,0.019,0.019,-0.213,-0.103,
> > >
> > >
> >
> 0.132,-0.498,0.132,0.777,-0.814,0.0,-0.498,0.132,-0.103,0.132,0.5973,-0.5679,
> > >
> > >
> >
> -0.4157,0.2719,0.0145,0.0779,-0.0398,-0.0173,-0.0173,0.0136,-0.0425,-0.0425,
> > >
> > >
> >
> 0.8054,-0.8188,-0.8188,0.0,0.5973,-0.5679,0.0,0.0,0.0,-0.4157,0.2719,0.0145,
> > >
> > >
> >
> 0.0779,-0.0071,0.0256,0.0256,-0.0174,0.043,0.043,0.6801,-0.5838,-0.6511,0.4641,
> > >
> > >
> >
> 0.5973,-0.5679,0.0,0.0,0.0,-0.4157,0.2719,0.0145,0.0779,-0.0071,0.0256,0.0256,
> > >
> > >
> >
> -0.0174,0.043,0.043,0.6801,-0.5838,-0.6511,0.0,0.5973,-0.5679,0.4641,0.0,0.0,
> > >
> > >
> >
> -0.4157,0.2719,0.0145,0.0779,-0.0071,0.0256,0.0256,-0.0174,0.043,0.043,0.6801,
> > >
> > >
> >
> -0.6511,-0.5838,0.0,0.5973,-0.5679,0.0,0.4641,0.0,-0.4157,0.2719,0.0145,0.0779,
> > >
> > >
> >
> -0.0071,0.0256,0.0256,-0.0174,0.043,0.043,0.6801,-0.6511,-0.5838,0.0,0.5973,
> > >
> > >
> >
> -0.5679,0.0,0.0,0.4641,-0.4157,0.2719,0.0341,0.0864,-0.1783,-0.0122,-0.0122,
> > >
> > >
> >
> 0.7994,-0.8014,-0.8014,0.0,0.5973,-0.5679,0.0,0.0,0.0,-0.4157,0.2719,0.0341,
> > >
> > >
> >
> 0.0864,-0.0316,0.0488,0.0488,0.6462,-0.5554,-0.6376,0.4747,0.5973,-0.5679,0.0,
> > >
> >
> 0.0,0.0,-0.4157,0.2719,0.0341,0.0864,-0.0316,0.0488,0.0488,0.6462,-0.5554,
> > >
> > >
> >
> -0.6376,0.0,0.5973,-0.5679,0.4747,0.0,0.0,-0.4157,0.2719,0.0341,0.0864,-0.0316,
> > >
> > >
> >
> 0.0488,0.0488,0.6462,-0.6376,-0.5554,0.0,0.5973,-0.5679,0.0,0.4747,0.0,-0.4157,
> > >
> > >
> >
> 0.2719,0.0341,0.0864,-0.0316,0.0488,0.0488,0.6462,-0.6376,-0.5554,0.0,0.5973,
> > > -0.5679,0.0,0.0,0.4747,
> > > PROTCNT=1,0,0,1,1,1,1,0,1,1,1,1,
> > > RESNAME='System: Unknown','Residue: TYR 29','Residue: TYR 44',
> > > 'Residue: TYR 51','Residue: TYR 75','Residue: TYR 128','Residue: TYR
> > 155',
> > > 'Residue: TYR 283','Residue: TYR 295','Residue: TYR 323','Residue: TYR
> > > 331',
> > > 'Residue: GL4 350','Residue: TYR 375','Residue: TYR 383','Residue: TYR
> > > 406',
> > > 'Residue: TYR 408','Residue: AS4 417',
> > > RESSTATE=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
> > > STATEINF(0)%FIRST_ATOM=482, STATEINF(0)%FIRST_CHARGE=0,
> > > STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=21,
> > > STATEINF(0)%NUM_STATES=2,
> > > STATEINF(1)%FIRST_ATOM=733, STATEINF(1)%FIRST_CHARGE=0,
> > > STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=21,
> > > STATEINF(1)%NUM_STATES=2,
> > > STATEINF(2)%FIRST_ATOM=850, STATEINF(2)%FIRST_CHARGE=0,
> > > STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=21,
> > > STATEINF(2)%NUM_STATES=2,
> > > STATEINF(3)%FIRST_ATOM=1225, STATEINF(3)%FIRST_CHARGE=0,
> > > STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=21,
> > > STATEINF(3)%NUM_STATES=2,
> > > STATEINF(4)%FIRST_ATOM=2086, STATEINF(4)%FIRST_CHARGE=0,
> > > STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=21,
> > > STATEINF(4)%NUM_STATES=2,
> > > STATEINF(5)%FIRST_ATOM=2515, STATEINF(5)%FIRST_CHARGE=0,
> > > STATEINF(5)%FIRST_STATE=0, STATEINF(5)%NUM_ATOMS=21,
> > > STATEINF(5)%NUM_STATES=2,
> > > STATEINF(6)%FIRST_ATOM=4616, STATEINF(6)%FIRST_CHARGE=0,
> > > STATEINF(6)%FIRST_STATE=0, STATEINF(6)%NUM_ATOMS=21,
> > > STATEINF(6)%NUM_STATES=2,
> > > STATEINF(7)%FIRST_ATOM=4804, STATEINF(7)%FIRST_CHARGE=0,
> > > STATEINF(7)%FIRST_STATE=0, STATEINF(7)%NUM_ATOMS=21,
> > > STATEINF(7)%NUM_STATES=2,
> > > STATEINF(8)%FIRST_ATOM=5242, STATEINF(8)%FIRST_CHARGE=0,
> > > STATEINF(8)%FIRST_STATE=0, STATEINF(8)%NUM_ATOMS=21,
> > > STATEINF(8)%NUM_STATES=2,
> > > STATEINF(9)%FIRST_ATOM=5373, STATEINF(9)%FIRST_CHARGE=0,
> > > STATEINF(9)%FIRST_STATE=0, STATEINF(9)%NUM_ATOMS=21,
> > > STATEINF(9)%NUM_STATES=2,
> > > STATEINF(10)%FIRST_ATOM=5702, STATEINF(10)%FIRST_CHARGE=42,
> > > STATEINF(10)%FIRST_STATE=2, STATEINF(10)%NUM_ATOMS=19,
> > > STATEINF(10)%NUM_STATES=5, STATEINF(11)%FIRST_ATOM=6107,
> > > STATEINF(11)%FIRST_CHARGE=0, STATEINF(11)%FIRST_STATE=0,
> > > STATEINF(11)%NUM_ATOMS=21, STATEINF(11)%NUM_STATES=2,
> > > STATEINF(12)%FIRST_ATOM=6246, STATEINF(12)%FIRST_CHARGE=0,
> > > STATEINF(12)%FIRST_STATE=0, STATEINF(12)%NUM_ATOMS=21,
> > > STATEINF(12)%NUM_STATES=2, STATEINF(13)%FIRST_ATOM=6645,
> > > STATEINF(13)%FIRST_CHARGE=0, STATEINF(13)%FIRST_STATE=0,
> > > STATEINF(13)%NUM_ATOMS=21, STATEINF(13)%NUM_STATES=2,
> > > STATEINF(14)%FIRST_ATOM=6685, STATEINF(14)%FIRST_CHARGE=0,
> > > STATEINF(14)%FIRST_STATE=0, STATEINF(14)%NUM_ATOMS=21,
> > > STATEINF(14)%NUM_STATES=2, STATEINF(15)%FIRST_ATOM=6817,
> > > STATEINF(15)%FIRST_CHARGE=137, STATEINF(15)%FIRST_STATE=7,
> > > STATEINF(15)%NUM_ATOMS=16, STATEINF(15)%NUM_STATES=5,
> > >
> > STATENE=0.000000,-65.113428,0.000000,8.405779,8.405779,8.405779,8.405779,
> > > 0.000000,26.889458,26.889458,26.889458,26.889458,
> > >
> > >
> >
> PKA_CORR=9.6000,0.0000,0.0000,4.4000,4.4000,4.4000,4.4000,0.0000,4.0000,4.0000,
> > > 4.0000,4.0000,
> > > TRESCNT=16,
> > > /
> > > [r11831vd.hlogin2 [csf3] 3A4]$
> > >
> > > --
> > >
> > > Regards,
> > >
> > > Dr. Vaibhav A. Dixit,
> > >
> > > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> > The
> > > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > > AND
> > > Assistant Professor,
> > > Department of Pharmacy,
> > > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > > India.
> > > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > > Email: vaibhav.dixit.pilani.bits-pilani.ac.in<mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>, vaibhavadixit.gmail.com<mailto:vaibhavadixit.gmail.com>
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> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Thu May 30 2019 - 13:00:02 PDT
