AMBER Archive (2008)

Subject: AMBER: bond breaking in proteins

From: Eddie Mende (pckboy_at_gmail.com)
Date: Tue Feb 26 2008 - 16:41:22 CST

Hello ,

I am trying to do a QM/MM molecular dynamics simulation. My final goal
is to do free energy simulations, but first I want to check that the
molecular
dynamics behavior seems acceptable.

1) A simple MM simulation gives me a good starting structure,
I ran this for 10 PS, the structure is equilibrated :
MD equilibration from t0 to 10 K
&cntrl
imin=0, irest=0,
nstlim=10000,dt=0.001, ntc=1,
ntpr=50, ntwx=50, ntwv=50,
cut=20, ntb=0, igb=1,
ntt=3, gamma_ln=2.0,
tempi=200.0, temp0=200.0,
/
   A V E R A G E S O V E R 10000 S T E P S

NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 199.56 PRESS
= 0.0
Etot = -1184.2709 EKtot = 772.1212 EPtot =
-1956.3921
BOND = 314.4925 ANGLE = 477.2611 DIHED =
839.3245
1-4 NB = 269.8956 1-4 EEL = 3841.7548 VDWAALS =
-626.7479
EELEC = -5502.4007 EGB = -1569.9719 RESTRAINT =
0.0000
------------------------------------------------------------------------------

    R M S F L U C T U A T I O N S

NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 4.59 PRESS
= 0.0
Etot = 19.1454 EKtot = 17.7577 EPtot =
18.8241
BOND = 16.2280 ANGLE = 16.1669 DIHED =
9.0737
1-4 NB = 6.3145 1-4 EEL = 13.9071 VDWAALS =
10.8267
EELEC = 143.1958 EGB = 139.5329 RESTRAINT =
0.0000
------------------------------------------------------------------------------

2) Then I take the final structure, and use a QM/MM MD script.
the problem is that the PO3 group attached to HIS15 no longer stays
attached to the Nitrogen,
but flyes away this is totally unexpected....this PO3 group should be
fairly stable at that temperature,
this even happens at lower temperatures i.e. 100K. Phosphoryl release
should only be possible
at those temperatures via catalysis....so I can not pursue the matter
further until I find what is wrong.
I was thinking that at least I should add a few explicit salvation
shells, but maybe I am doing something
wrong with the cutoffs,etc. At the end of the day, my goal is to
evaluate the free energy of
HIS15-PO3 bond breaking.

MD equilibration from t0 to 200 K
&cntrl
imin=0, irest=0,
nstlim=10000,dt=0.001, ntc=1,
ntpr=50, ntwx=50, ntwv=50,
cut=15, ntb=0, igb=1,
ntt=3, gamma_ln=2.0,
tempi=200.0, temp0=200.0,
ifqnt=1
/
&qmmm
qmmask=':12,13,14,15,16',
qmcharge=0,
qmtheory=3, qmcut=20.0, WRITEPDB=1, PRINTCHARGES=1,
/

REMARK QM region, initial structure
ATOM 1 N QM 1 10.078 -4.502 6.346
ATOM 2 H QM 1 9.922 -3.824 7.079
ATOM 3 C QM 1 9.513 -4.191 5.032
ATOM 4 H QM 1 9.689 -5.021 4.349
ATOM 5 C QM 1 7.997 -4.015 5.202
ATOM 6 H QM 1 7.805 -3.245 5.952
ATOM 7 H QM 1 7.554 -3.687 4.262
ATOM 8 C QM 1 7.324 -5.325 5.610
ATOM 9 O QM 1 7.712 -6.415 5.203
ATOM 10 N QM 1 6.290 -5.265 6.427
ATOM 11 H QM 1 5.851 -6.128 6.709
ATOM 12 H QM 1 5.953 -4.374 6.756
ATOM 13 C QM 1 10.167 -2.964 4.375
ATOM 14 O QM 1 9.728 -2.538 3.300
ATOM 15 N QM 1 11.206 -2.399 5.008
ATOM 16 H QM 1 11.520 -2.804 5.882
ATOM 17 C QM 1 11.778 -1.123 4.611
ATOM 18 H QM 1 12.715 -0.950 5.144
ATOM 19 H QM 1 11.974 -1.134 3.537
ATOM 20 C QM 1 10.802 0.018 4.937
ATOM 21 O QM 1 9.681 -0.223 5.427
ATOM 22 N QM 1 11.277 1.252 4.666
ATOM 23 H QM 1 12.097 1.281 4.088
ATOM 24 C QM 1 10.419 2.406 4.780
ATOM 25 H QM 1 9.750 2.246 5.672
ATOM 26 C QM 1 11.290 3.681 5.034
ATOM 27 H QM 1 12.226 3.401 5.557
ATOM 28 H QM 1 11.593 4.073 4.039
ATOM 29 C QM 1 10.550 4.780 5.820
ATOM 30 H QM 1 9.453 4.712 5.580
ATOM 31 C QM 1 10.683 4.560 7.332
ATOM 32 H QM 1 11.742 4.600 7.650
ATOM 33 H QM 1 10.110 5.320 7.900
ATOM 34 H QM 1 10.286 3.569 7.642
ATOM 35 C QM 1 11.024 6.226 5.365
ATOM 36 H QM 1 10.831 6.329 4.287
ATOM 37 H QM 1 10.429 6.955 5.938
ATOM 38 H QM 1 12.093 6.293 5.615
ATOM 39 C QM 1 9.540 2.583 3.521
ATOM 40 O QM 1 9.844 3.163 2.495
ATOM 41 N QM 1 8.215 2.050 3.595
ATOM 42 H QM 1 7.964 1.478 4.366
ATOM 43 C QM 1 7.215 2.177 2.555
ATOM 44 H QM 1 7.716 2.393 1.556
ATOM 45 C QM 1 6.464 0.821 2.355
ATOM 46 H QM 1 6.018 0.906 1.336
ATOM 47 H QM 1 7.205 -0.008 2.230
ATOM 48 C QM 1 5.447 0.349 3.373
ATOM 49 N QM 1 4.069 0.361 3.126
ATOM 50 C QM 1 3.444 -0.232 4.258
ATOM 51 H QM 1 2.381 -0.283 4.365
ATOM 52 N QM 1 4.417 -0.751 5.189
ATOM 53 H QM 1 4.224 -0.293 6.101
ATOM 54 C QM 1 5.654 -0.174 4.653
ATOM 55 H QM 1 6.522 -0.159 5.301
ATOM 56 P QM 1 3.164 1.139 1.727
ATOM 57 O QM 1 3.761 0.366 0.602
ATOM 58 O QM 1 1.789 0.794 2.191
ATOM 59 O QM 1 3.646 2.541 1.903
ATOM 60 H QM 1 3.167 -0.314 0.309
ATOM 61 C QM 1 6.287 3.385 2.857
ATOM 62 O QM 1 6.530 4.218 3.721
ATOM 63 N QM 1 5.265 3.648 1.884
ATOM 64 H QM 1 4.889 2.777 1.577
ATOM 65 C QM 1 4.193 4.619 2.161
ATOM 66 H QM 1 4.701 5.599 1.829
ATOM 67 C QM 1 2.936 4.469 1.183
ATOM 68 H QM 1 2.279 3.679 1.630
ATOM 69 C QM 1 2.034 5.729 1.172
ATOM 70 H QM 1 2.573 6.648 0.842
ATOM 71 H QM 1 1.144 5.510 0.545
ATOM 72 H QM 1 1.631 5.857 2.205
ATOM 73 O QM 1 3.373 4.176 -0.102
ATOM 74 H QM 1 2.755 3.660 -0.610
ATOM 75 C QM 1 3.714 4.840 3.594
ATOM 76 O QM 1 3.655 5.937 4.109
ATOM 77 H QM 1 10.683 -5.379 6.574
ATOM 78 H QM 1 3.274 4.018 4.159
END

REMARK Posphorylated Histidine after 1 ps.
REMARK
(:15);
ATOM 216 N H1D 15 9.131 1.736
2.835 N
ATOM 217 H H1D 15 8.831 1.747
3.881 H
ATOM 218 CA H1D 15 8.081 2.156
1.748 CT
ATOM 219 HA H1D 15 8.682 2.563
0.950 H1
ATOM 220 CB H1D 15 7.434 0.843
1.051 CT
ATOM 221 HB2 H1D 15 6.783 1.175
0.204 HC
ATOM 222 HB3 H1D 15 8.273 0.403
0.516 HC
ATOM 223 CG H1D 15 6.749 -0.120
1.912 CC
ATOM 224 ND1 H1D 15 5.509 0.377
2.613 NA
ATOM 225 CE1 H1D 15 5.122 -0.646
3.361 CR
ATOM 226 HE1 H1D 15 4.337 -0.684
4.197 H5
ATOM 227 NE2 H1D 15 6.001 -1.751
3.157 NA
ATOM 228 HE2 H1D 15 5.892 -2.627
3.623 H
ATOM 229 CD2 H1D 15 6.964 -1.417
2.221 CW
ATOM 230 HD2 H1D 15 7.763 -2.136
1.911 H4
ATOM 231 P H1D 15 0.053 -2.288
0.132 P
ATOM 232 O1P H1D 15 -0.454 -3.723
0.592 OH
ATOM 233 O2P H1D 15 -0.630 -1.042
0.470 O2
ATOM 234 O3P H1D 15 1.472 -2.070
-0.431 O2
ATOM 235 H1P H1D 15 0.273 -4.390
0.611 HO
ATOM 236 C H1D 15 6.980 3.077
2.387 C
ATOM 237 O H1D 15 7.216 3.662
3.418 O
END And here is the whole protein (attached PHPrp.pdb)

Now, the definition for the Phosphorylated histidine is taken from here:
http://pharmacy.man.ac.uk/amber/ .... (H1D protonated)....by the way,
if I try the unprotonated
one, the PO3 flyes away too even in regular MM simulations, perhaps this
is telling me I should
include explicit water?.

Thanks for the feedback!

Eduardo Mendez

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