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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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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 - 05:30:02 PDT
