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,-0.103,0.132,0.5973,-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 Mon Aug 21 2017 - 09:00:03 PDT
