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>. 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>.
> > > > 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
> >.
> > > > 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
> > > > 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
> > > > _______________________________________________
> > > > AMBER mailing list
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> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > 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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> >
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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
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 Thu May 30 2019 - 08:00:02 PDT
