Re: [AMBER] Deprotonation of Tyr using Parmed

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Tue, 22 Aug 2017 14:08:06 +0000

Dear Marcos,
I think I figured out.
I run these commands to check the charges on TYR "HH", it is zero as expected.

parmed -p model_sol.altered.parm7 -c model_sol.altered.rst7 <<_EOF

printDetails .7780-7800
_EOF


                                  /^^^/ /]
                                 / ] / ]
                         _______/ ]___ / ]
                        / \_____/ /
                      _/ [.] \ \ \
                     /.. | | ]
                      VVVvvv\ | | _/\ ]
          P A R M E D | / \ ]
                     AAA^^^^^ / \]
                      \_________\ \_____/
                                \ \
                                 \____\

ParmEd: a Parameter file Editor


Loaded Amber topology file model_sol.altered.parm7 with coordinates from model_sol.altered.rst7

Reading input from STDIN...
> >
The mask .7780-7800 matches 21 atoms:

   ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass Charge GB Radius GB Screen
   7780 517 TYR N N 7 1.8240 0.1700 14.0100 -0.4157 1.5500 0.7900
   7781 517 TYR H H 1 0.6000 0.0157 1.0080 0.2719 1.3000 0.8500
   7782 517 TYR CA CX 6 1.9080 0.1094 12.0100 -0.0014 1.7000 0.7200
   7783 517 TYR HA H1 1 1.3870 0.0157 1.0080 0.0876 1.2000 0.8500
   7784 517 TYR CB CT 6 1.9080 0.1094 12.0100 -0.0858 1.7000 0.7200
   7785 517 TYR HB2 HC 1 1.4870 0.0157 1.0080 0.0190 1.2000 0.8500
   7786 517 TYR HB3 HC 1 1.4870 0.0157 1.0080 0.0190 1.2000 0.8500
   7787 517 TYR CG CA 6 1.9080 0.0860 12.0100 -0.2130 1.7000 0.7200
   7788 517 TYR CD1 CA 6 1.9080 0.0860 12.0100 -0.1030 1.7000 0.7200
   7789 517 TYR HD1 HA 1 1.4590 0.0150 1.0080 0.1320 1.2000 0.8500
   7790 517 TYR CE1 CA 6 1.9080 0.0860 12.0100 -0.4980 1.7000 0.7200
   7791 517 TYR HE1 HA 1 1.4590 0.0150 1.0080 0.1320 1.2000 0.8500
   7792 517 TYR CZ C 6 1.9080 0.0860 12.0100 0.7770 1.7000 0.7200
   7793 517 TYR OH OH 8 1.7210 0.2104 16.0000 -0.8140 1.5000 0.8500
   7794 517 TYR HH HO 1 0.0000 0.0000 1.0080 0.0000 1.2000 0.8500
   7795 517 TYR CE2 CA 6 1.9080 0.0860 12.0100 -0.4980 1.7000 0.7200
   7796 517 TYR HE2 HA 1 1.4590 0.0150 1.0080 0.1320 1.2000 0.8500
   7797 517 TYR CD2 CA 6 1.9080 0.0860 12.0100 -0.1030 1.7000 0.7200
   7798 517 TYR HD2 HA 1 1.4590 0.0150 1.0080 0.1320 1.2000 0.8500
   7799 517 TYR C C 6 1.9080 0.0860 12.0100 0.5973 1.7000 0.7200
   7800 517 TYR O O 8 1.6612 0.2100 16.0000 -0.5679 1.5000 0.8500

thank you.
Regards
SOwmya

________________________________________
From: Sowmya Indrakumar
Sent: Tuesday, August 22, 2017 3:41 PM
To: AMBER Mailing List
Subject: RE: [AMBER] Deprotonation of Tyr using Parmed

Dear Marcos,
Thanks for you're suggestions.

This is what I tried. using the parameter and topology files generated from H++ at the desired pH, I run parmed "changeProtstate" command to change the protonated TYR to deprotonated TYR form.

These are the commands:parmed -p model_sol.parm7 -c model_sol.rst7 <<_EOF
> changeProtState .1415-1435 1
> changeProtState .2786-2806 1
> changeProtState .6410-6430 1
> changeProtState .7780-7800 1
> parmout model_sol.altered.parm7 model_sol.altered.rst7
> _EOF

                                  /^^^/ /]
                                 / ] / ]
                         _______/ ]___ / ]
                        / \_____/ /
                      _/ [.] \ \ \
                     /.. | | ]
                      VVVvvv\ | | _/\ ]
          P A R M E D | / \ ]
                     AAA^^^^^ / \]
                      \_________\ \_____/
                                \ \
                                 \____\

ParmEd: a Parameter file Editor


Loaded Amber topology file model_sol.parm7 with coordinates from model_sol.rst7

Reading input from STDIN...
> Changing protonation state of residue 95 (TYR) to 1
> Changing protonation state of residue 188 (TYR) to 1
> Changing protonation state of residue 426 (TYR) to 1
> Changing protonation state of residue 517 (TYR) to 1
> > Outputting Amber topology file model_sol.altered.parm7 and restart model_sol.altered.rst7
Done!


the PDB file from: ambpdb -p model_sol.altered.parm7 -c restart model_sol.altered.rst7 > model.pdb, TYRs still exist as Protonated. Ideally, the HH atom record should have disappered. Is it something wrong I am doing?

ATOM 1415 N TYR 95 48.608 43.117 57.661 1.00 0.00 N
ATOM 1416 H TYR 95 49.228 43.202 56.867 1.00 0.00 H
ATOM 1417 CA TYR 95 49.122 42.559 58.899 1.00 0.00 C
ATOM 1418 HA TYR 95 48.685 43.093 59.745 1.00 0.00 H
ATOM 1419 CB TYR 95 48.741 41.081 59.036 1.00 0.00 C
ATOM 1420 HB2 TYR 95 49.170 40.683 59.955 1.00 0.00 H
ATOM 1421 HB3 TYR 95 47.657 41.010 59.137 1.00 0.00 H
ATOM 1422 CG TYR 95 49.174 40.208 57.878 1.00 0.00 C
ATOM 1423 CD1 TYR 95 50.366 39.487 57.933 1.00 0.00 C
ATOM 1424 HD1 TYR 95 51.015 39.592 58.790 1.00 0.00 H
ATOM 1425 CE1 TYR 95 50.752 38.667 56.886 1.00 0.00 C
ATOM 1426 HE1 TYR 95 51.684 38.123 56.933 1.00 0.00 H
ATOM 1427 CZ TYR 95 49.935 38.567 55.773 1.00 0.00 C
ATOM 1428 OH TYR 95 50.305 37.782 54.739 1.00 0.00 O
ATOM 1429 HH TYR 95 51.147 37.344 54.884 1.00 0.00 H
ATOM 1430 CE2 TYR 95 48.754 39.256 55.686 1.00 0.00 C
ATOM 1431 HE2 TYR 95 48.143 39.164 54.803 1.00 0.00 H
ATOM 1432 CD2 TYR 95 48.374 40.075 56.746 1.00 0.00 C
ATOM 1433 HD2 TYR 95 47.459 40.639 56.679 1.00 0.00 H
ATOM 1434 C TYR 95 50.636 42.787 58.977 1.00 0.00 C
ATOM 1435 O TYR 95 51.229 43.279 58.023 1.00 0.00 O


Kindly, comment on this.
Thanks
Regards
Sowmya
________________________________________
From: Marcos Serrou do Amaral [marcossamaral.gmail.com]
Sent: Tuesday, August 22, 2017 1:25 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Deprotonation of Tyr

Hi Sowmya!

>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)

The state 0 for TYR is the protonated state (pKa=9.6).

>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 ??

I guess so. When you say that you want the TYR residue, the leap will
provide you the titratable TYR residue for CpHMD simulations.

I believe that it should be a good idea to use parmed to set the TYR and
LYS initial states (changeProtState), instead to use it only on cpin file.

Regards
---
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/amber
Received on Tue Aug 22 2017 - 07:30:03 PDT
Custom Search