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--- 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 > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > > AMBER mailing list > > 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 > _______________________________________________ > 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/amberReceived on Thu May 30 2019 - 06:00:02 PDT