Sowmya,
Sorry for late reply, both cc'ed email didn't arrive in Inbox.
If you want to keep specific TYR and LYS in deprotonated or protonated
state through out constant pH MD simulation then do not put them in
titrating residue list. When you are creating cpin file by using
cpinutil.py, do not mention those residue names.
In CpHMD/pH-REMD protocol, titratable residues are parametrized with all
possible protons. These protons retain their position through out CpHMD
simulation. Suppose Tyr is in protonated state and during CpHMD, it was
allowed to change into deprotonated state. Then zero charge will be
assigned to titratable proton and charges on backbone and side-chain atoms
will be updated according to deprotonated state of Tyr residue. (Read
protonation State Models section in this paper -
http://doi.wiley.com/10.1002/jcc.20139 )
CpHMD/pH-REMD prmtop and trajectory files will have all titratable protons
atomtypes and co-ordinates irrespective of protonation state. That's why,
Tyr's titratable proton co-ordinates were there in pdb file. Protonation
state information of residue will only be in cpout files. That's why, to
analyze CpHMD/pH-REMD trajectories, cpout and trajectories files must be
used together. One example is given here-
http://ambermd.org/tutorials/advanced/tutorial18/section4.htm. In this
example, a tcl script has been written by using cpout files which will
delete all "ghost" protons while visualizing in vmd.
Let me know if it clear some doubts,
Pancham Lal
PhD, Department of Chemistry
University of Florida
On Sun, Aug 20, 2017 at 9:45 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
wrote:
> Dear All,
>
> I want to keep certain TYR in the deprotonated state and one LYS
> protonated while performing constpH MD at pH=7.4 and IS= 0.1M
>
> I generated the initial cpin file and a new parameter file using the below
> mentioned command:
>
> cpinutil.py -p model_sol.parm7 -igb 2 -o model_sol.cpin -op
> model_sol.mod0.parm7 -resnums 95 188 426 517 296 -states 1 1 1 1 0
>
>
> This is how my cpin file looks:
>
> &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,-0.103,0.1
> 32,0.5973,-0.5679,
> -0.3479,0.2747,-0.24,0.1426,-0.0094,0.0362,0.0362,0.0187,0.
> 0103,0.0103,-0.0479,
> 0.0621,0.0621,-0.0143,0.1135,0.1135,-0.3854,0.34,0.34,0.34,
> 0.7341,-0.5894,
> -0.3479,0.2747,-0.24,0.1426,-0.10961,0.034,0.034,0.06612,0.01041,0.01041,
> -0.03768,0.01155,0.01155,0.32604,-0.03358,-0.03358,-1.03581,0.0,0.38604,
> 0.38604,0.7341,-0.5894,
> PROTCNT=0,3,
> RESNAME='System: Unknown','Residue: TYR 95','Residue: TYR 188',
> 'Residue: LYS 296','Residue: TYR 426','Residue: TYR 517',
> RESSTATE=1,1,1,1,0,
> STATEINF(0)%FIRST_ATOM=1415, STATEINF(0)%FIRST_CHARGE=0,
> STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=21,
> STATEINF(0)%NUM_STATES=2,
> STATEINF(1)%FIRST_ATOM=2786, STATEINF(1)%FIRST_CHARGE=0,
> STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=21,
> STATEINF(1)%NUM_STATES=2,
> STATEINF(2)%FIRST_ATOM=4476, STATEINF(2)%FIRST_CHARGE=42,
> STATEINF(2)%FIRST_STATE=2, STATEINF(2)%NUM_ATOMS=22,
> STATEINF(2)%NUM_STATES=2,
> STATEINF(3)%FIRST_ATOM=6410, STATEINF(3)%FIRST_CHARGE=0,
> STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=21,
> STATEINF(3)%NUM_STATES=2,
> STATEINF(4)%FIRST_ATOM=7780, STATEINF(4)%FIRST_CHARGE=0,
> STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=21,
> STATEINF(4)%NUM_STATES=2,
> STATENE=0.000000,-78.199991,-0.845507,0.000000,
> TRESCNT=5,CPHFIRST_SOL=10324, CPH_IGB=2, CPH_INTDIEL=1.0,
> /
>
> I manually changed the cpin file " PROTCNT=1,0,3,2," to PROTCNT="0,3," to
> only consider deprotonated TYR and protonated LYS. Is this the right way?
>
>
> After the equilibration step, *.cpout file looks like this for all time
> steps:
>
> Solvent pH: 7.40000
> Monte Carlo step size: 500
> Time step: 500
> Time: 1000.998
> Residue 0 State: 0
> Residue 1 State: 0
> Residue 2 State: 0
> Residue 3 State: 0
> Residue 4 State: 0
>
> Residue 0 State: 0
> Residue 1 State: 0
> Residue 2 State: 0
> Residue 3 State: 0
> Residue 4 State: 0
>
> Residue 0 State: 0
> Residue 1 State: 0
> Residue 2 State: 0
> Residue 3 State: 0
> Residue 4 State: 0
>
> Residue 0 State: 0
> Residue 1 State: 0
> Residue 2 State: 0
> Residue 3 State: 0
> Residue 4 State: 0
>
> Does the State 0 above mean, the default state which I have mentioned in
> the cpin file??
>
> Ideally, when I take any random frame after equilibration step and
> generate a pdb, I should have the deprotonated TYR 95 atom record. But I
> see the proton present.
>
> ATOM 1415 N TYR 95 50.406 44.914 56.235 1.00 0.00
> N
> ATOM 1416 H TYR 95 50.688 44.636 55.305 1.00 0.00
> H
> ATOM 1417 CA TYR 95 51.132 44.350 57.398 1.00 0.00
> C
> ATOM 1418 HA TYR 95 50.852 44.846 58.327 1.00 0.00
> H
> ATOM 1419 CB TYR 95 50.486 42.938 57.435 1.00 0.00
> C
> ATOM 1420 HB2 TYR 95 50.764 42.428 58.358 1.00 0.00
> H
> ATOM 1421 HB3 TYR 95 49.403 43.058 57.460 1.00 0.00
> H
> ATOM 1422 CG TYR 95 50.962 41.963 56.336 1.00 0.00
> C
> ATOM 1423 CD1 TYR 95 52.192 41.330 56.655 1.00 0.00
> C
> ATOM 1424 HD1 TYR 95 52.737 41.608 57.544 1.00 0.00
> H
> ATOM 1425 CE1 TYR 95 52.756 40.465 55.709 1.00 0.00
> C
> ATOM 1426 HE1 TYR 95 53.777 40.165 55.897 1.00 0.00
> H
> ATOM 1427 CZ TYR 95 52.155 40.250 54.423 1.00 0.00
> C
> ATOM 1428 OH TYR 95 52.880 39.621 53.479 1.00 0.00
> O
> ATOM 1429 HH TYR 95 52.243 39.414 52.791 1.00 0.00
> H
> ATOM 1430 CE2 TYR 95 50.991 40.970 54.148 1.00 0.00
> C
> ATOM 1431 HE2 TYR 95 50.645 41.009 53.126 1.00 0.00
> H
> ATOM 1432 CD2 TYR 95 50.363 41.795 55.070 1.00 0.00
> C
> ATOM 1433 HD2 TYR 95 49.499 42.394 54.825 1.00 0.00
> H
> ATOM 1434 C TYR 95 52.628 44.429 57.246 1.00 0.00
> C
>
> I kindly need you're comments on this.
>
> Thanks
> Regards
> Sowmya
> ________________________________________
> From: Sowmya Indrakumar [soemya.kemi.dtu.dk]
> Sent: Friday, August 18, 2017 5:24 PM
> To: amber.ambermd.org
> Subject: [AMBER] Deprotonation of Tyr
>
> Dear All,
> I wish to perform simulations with varying salt concentration of NaCl of
> upto 200mM at a particular pH=7. I want to keep some of the Tyrosines in
> the deprotonated state.
>
> So here, my question is, Can I perform these simulations using constant pH
> MD? Because, I think concentrations can be adjusted to upto 0.1M.
>
> Is there any other way to consider doing the deprotonation?
> Kindly, give me you're suggestion in this regard.
> Regards
> Sowmya
>
>
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Received on Wed Aug 30 2017 - 09:00:02 PDT
