Custom Search
--- Marcos S.A. On Mon, Aug 21, 2017 at 4:19 PM, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote: > Dear Marcos, > Thank you for you're suggestions. > > Could you please explain me why you mentioned -state 0 for the TYRs ?? The > default 0 flag in case of TYR is for the protonated state (mentioned in > manual) > > Also, should the initial pdb file which I use to generate topology and > parameter files, should those specific TYRs already have the deprotonated > atom record ?? > > Thank you. > Regards > Sowmya > ________________________________________ > From: Marcos Serrou do Amaral [marcossamaral.gmail.com] > Sent: Monday, August 21, 2017 9:34 PM > To: AMBER Mailing List > Subject: Re: [AMBER] Deprotonation of Tyr > > Dear Sowmya, > I am not sure how to do that, but I would try: > > cpinutil.py -p model_sol.parm7 -igb 2 -o model_sol.cpin -op > model_sol.mod0.parm7 -resnums 95 188 296 426 517 -states 0 0 0 0 0 > > and then try to change your cpin file: > > STATENE=0.000000,-78.199991,-0.845507,0.000000, > TO > STATENE=0.000000,99.99,-99.99,0.000000, > > Good luck! > > --- > Marcos S.A. > > > On Mon, Aug 21, 2017 at 11:37 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. > > 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 > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 > _______________________________________________ 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 Tue Aug 22 2017 - 07:00:02 PDT