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
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Received on Thu May 30 2019 - 05:00:01 PDT
