Re: [AMBER] empty cein file redox potential calculations from Vaibhav Dixit on 2020-01-06 (Amber Archive Jan 2020)

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 6 Jan 2020 17:59:37 +0900

Dear Cruzeiro,Vinicius, and all,
I now have time and resource to start work on this again.
But I have the following doubts about defining the Heme redox active states.
1) I'm thinking of running G09 jobs to find charges for oxd-red states of
Heme center using b3lyp/6-31+G(d,p) and lanld2z pseudo potentials on Fe. I
want to include CYS (bound to Fe) in QM calculations since there are
changes in charge-spin states on S. So here Heme-CYS would become one unit
for AmberTools. is this correct? But in PDBs like 1W0E the CYS and HEM
separate, so do I change atom/residue numbers for CYS in the PDB while
generating prmtop?
2) The HEM in 1W0E has propionates (as in 1hrc amber-tutorial), these are
required during G09 calculations to define charges for redox states? But
then how do I separate them, for defining ionizable residues later to
generate cein and cpin files and how the propionate (PRN) can become
separate residues once I have used them as part of Hem while defining Hem
charges? So is it possible/required to define heme charges without the
propionates (this can mess-up with the expected charge-spin states, thus
I'm not sure how to model this).

Can you please suggest me on how to think about and proceed for generating
parameters for CYP450s for doing ConspH-Redox MD simulations?

Thank you very much and
best regards (and a very happy and prosperous new year to all).

On Fri, May 31, 2019 at 4:29 AM Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:

> 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> 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>
> 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> 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
> >
> > > 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,
> vaibhavadixit.gmail.com
> > > > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
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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,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
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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,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
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> P Please consider the environment before printing this e-mail
>
>

-- 
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, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Mon Jan 06 2020 - 05:00:01 PST