Zitat von Jason Swails <jason.swails.gmail.com>:
> On Mon, Feb 3, 2014 at 6:55 AM, Schackert Nico <
> Nico.Schackert.student.uibk.ac.at> wrote:
>
>> Zitat von Jason Swails <jason.swails.gmail.com>:
>>
>> > On Tue, 2014-01-28 at 10:18 +0100, Schackert Nico wrote:
>> >> Dear AMBER users,
>> >>
>> >> I'm performing TI calculations in Amber12 with energy decomposition
>> >> (idecomp=1). Van der Waals and electrostatics contributions are fine,
>> >> but I do not get any internal energies; all values in that column
>> >> remain 0.
>> >> Is there anything I'm missing? Setting RRES seems to only cause
>> >> troubles with group numbers and residues therein.
>> >
>> > The manual says "All residues, including solvent molecules, have to be
>> > chosen by the RRES card to be considered for decomposition." so I would
>> > suggest changing the bottom of your input file to:
>> >
>> > LISTOUT=POUT
>> > DISANG=RESTRAINTS.dat
>> > decomposed residues
>> > RRES 1 6904
>> > END
>> > printed residues
>> > RES 1 6904
>> > END
>> > END
>> >
>> > If something doesn't work, it would help to know specifics in order to
>> > try helping.
>> >
>> > Also, the idecomp flag means something different in standard simulations
>> > than it does with TI. When running TI, the decomposed energies reflect
>> > dV/dlambda, not the total decomposed potential. Indeed, I would expect
>> > most of the internal terms to be 0, but a small number to be non-zero
>> > (depending on how far the 1-4 nonbonded interactions extend from your
>> > softcore mask).
>> >
>> > Good luck,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> Dear Jason,
>>
>> my system consits of 6904 residues. Residue 1-235 is my protein,
>> residue 236 is the ligand and the rest are water molecules. As you
>> mentioned I have chosen all residues in the RRES card. But running a
>> simulation with your proposed input file:
>>
>> > LISTOUT=POUT
>> > DISANG=RESTRAINTS.dat
>> > decomposed residues
>> > RRES 1 6904
>> > END
>> > printed residues
>> > RES 1 6904
>> > END
>> > END
>>
>> my out file looks like this:
>>
>> LOADING THE DECOMP ATOMS AS GROUPS
>>
>> ----- READING GROUP 1; TITLE:
>> decomposed residues
>> Number of atoms in this group = 0
>> ----- READING GROUP 2; TITLE:
>> printed residus
>> GRP 2 RES 1 TO 6904
>> Number of atoms in this group = 23731
>> ----- END OF GROUP READ -----
>> Atom 1 ( 1) : 6905 2
>> Atom 2 ( 1) : 6905 2
>> Atom 3 ( 1) : 6905 2
>> Atom 4 ( 1) : 6905 2
>> Atom 5 ( 1) : 6905 2
>> Atom 6 ( 1) : 6905 2
>> Atom 7 ( 1) : 1 2
>> Atom 8 ( 1) : 1 2
>> Atom 9 ( 1) : 1 2
>> Atom 10 ( 1) : 1 2
>> Atom 11 ( 1) : 1 2
>> Atom 12 ( 1) : 1 2
>> Atom 13 ( 1) : 1 2
>> Atom 14 ( 1) : 1 2
>> Atom 15 ( 1) : 1 2
>> Atom 16 ( 1) : 1 2
>> Atom 17 ( 1) : 1 2
>> Atom 18 ( 1) : 1 2
>> Atom 19 ( 1) : 1 2
>> Atom 20 ( 1) : 6905 2
>> Atom 21 ( 1) : 6905 2
>> Atom 22 ( 2) : 6906 2
>> ...
>> ...
>>
>> It seems that only the RES card is taken into account for the groups.
>> Also I don't understand the numbering.
>> Here are the result of the decomposition:
>>
>> PRINT DECOMP - TOTAL ENERGIES
>>
>> resid |internal |vdw |eel
>> ===================================================================
>> ...
>> TDC 181 0.000000000 -0.039814303 0.011181401
>> TDC 182 0.000000000 0.993866935 0.520425455
>> TDC 183 0.000000000 -0.009968909 0.003068046
>> TDC 184 0.000000000 -0.000124844 -0.088772571
>> TDC 185 0.000000000 -0.003128159 -0.009191419
>> TDC 186 0.000000000 -0.000057538 0.000340674
>> TDC 187 0.000000000 -0.000057538 0.003543921
>> TDC 188 0.000000000 -0.000110142 -0.001904374
>> TDC 189 0.000000000 -0.000144397 0.000843237
>> TDC 190 0.000000000 -0.000113869 0.000187873
>> TDC 191 0.000000000 -0.000106155 -0.000825267
>> TDC 192 0.000000000 -0.000168923 0.008043139
>> TDC 193 0.000000000 -0.000158241 -0.000284010
>> TDC 194 0.000000000 -0.000143302 0.004497833
>> TDC 195 0.000000000 -0.000111141 -0.008057381
>> TDC 196 0.000000000 -0.000106155 0.000550683
>> TDC 197 0.000000000 -0.000169766 -0.000021271
>> TDC 198 0.000000000 -0.000158241 -0.000169241
>> TDC 199 0.000000000 -0.000113869 0.000824396
>> TDC 200 0.000000000 -0.000106155 0.000474901
>> TDC 201 0.000000000 -0.000057538 -0.001028655
>> TDC 202 0.000000000 -0.000132505 0.002981423
>> TDC 203 0.000000000 -0.000113869 -0.001117164
>> TDC 204 0.000000000 -0.000087095 -0.006354657
>> TDC 205 0.000000000 -0.000307305 -0.005377947
>> TDC 206 0.000000000 -0.004231144 0.033327353
>> TDC 207 0.000000000 -0.001906100 0.096672786
>> TDC 208 0.000000000 -0.042354831 -0.045913426
>> TDC 209 0.000000000 -0.039700655 -0.005386305
>> TDC 210 0.000000000 -0.000076598 -0.000293246
>> TDC 211 0.000000000 -0.001612592 -0.307230580
>> TDC 212 0.000000000 -0.000143302 -0.023127391
>> TDC 213 0.000000000 -0.000057538 0.001771145
>> TDC 214 0.000000000 -0.000143302 -0.100324260
>> TDC 215 0.000000000 -0.000169766 0.009492851
>> TDC 216 0.000000000 -0.000057538 0.002683299
>> TDC 217 0.000000000 -0.000132505 -0.005621511
>> TDC 218 0.000000000 -0.000169766 -0.001170318
>> TDC 219 0.000000000 -0.000106155 0.000172590
>> TDC 220 0.000000000 -0.000143302 -0.006398194
>> TDC 221 0.000000000 -0.000113869 -0.000077377
>> TDC 222 0.000000000 -0.000106155 -0.000405005
>> TDC 223 0.000000000 -0.000076598 -0.000121663
>> TDC 224 0.000000000 -0.000158241 -0.000359945
>> TDC 225 0.000000000 -0.000132505 -0.000485589
>> TDC 226 0.000000000 -0.000143302 0.005511896
>> TDC 227 0.000000000 -0.000197399 -0.000308177
>> TDC 228 0.000000000 -0.000132505 -0.000203367
>> TDC 229 0.000000000 -0.000111141 -0.006959679
>> TDC 230 0.000000000 -0.000168923 0.004079400
>> TDC 231 0.000000000 -0.000087095 0.000124835
>> TDC 232 0.000000000 -0.000135643 -0.000230121
>> TDC 233 0.000000000 -0.000143302 0.006959990
>> TDC 234 0.000000000 -0.000118631 -0.006338392
>> TDC 235 0.000000000 -0.000004014 0.050514464
>> TDC 236 -196.933556611 -3.119493346 146.105557690
>> TDC 237 0.097499662 -0.000007500 0.097851217
>> TDC 238 0.000000000 -0.000012753 -0.001928825
>> TDC 239 0.000000000 -0.000012753 0.001365510
>> TDC 240 0.000000000 -0.000012753 -0.000693144
>> TDC 241 0.000000000 -0.000012753 0.001335047
>> TDC 242 0.000000000 -0.000012753 0.001450346
>> TDC 243 0.000000000 -0.000012753 -0.000199613
>> TDC 244 0.000000000 -0.000012753 0.003005742
>> ...
>>
>> I have a positive VdW interaction with RES 182 as supposed. But still
>> the values of the internal energies remain 0, except for the ligand
>> (RES 236) and the first water molecule (RES 237).
>> What is wrong? How can I understand this?
>>
>
> What is your scmask variable? As I said in my last email, TI decomposition
> details contributions to dV/dlambda for each residue, NOT the contribution
> of each residue to the total potential. Ergo if a mutation is occurring
> only in your ligand and the first water molecule (as I suspect), then only
> those two residues will have non-zero contributions to the internal
> dV/dlambda. All other internal terms are constant wrt to lambda, so
> dV/dlambda is zero. This also explains why the non-bonded values are so
> tiny for every other residue besides 236. The only values that contribute
> to the decomposed energies are basically the interactions of those residues
> with (only) the softcore region.
>
> Another thing that should stick out is that the contribution to the
> internal dV/dlambda is negative, and it is large negative. While
> technically a torsion potential can be negative (with a small value),
> bonds and angles can only be non-negative (and positive for all values
> other than the equilibrium bond or angle). -196 is virtually impossible
> for the bond+angle+torsion energy within a single residue, but is perfectly
> reasonable as a contribution to dV/dlambda.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dear Jason,
I am mutating a hydrogen into a methyl group in my ligand (res 236).
One ligand is called "IIA" and the second "IIP". Water molecules (res
237-6904) are not involved. Thats why I don't understand the internal
energy for res 237. Here are my two infiles.
disappear atom
&cntrl
ntx=5, irest=1,
ntwx=0, ntwr=20000,
ntb=2, cut=8,
nstlim=1000000, dt=0.001,
temp0=300, tempi=300, ntt=3, gamma_ln=2,
ntp=1, pres0=1, taup=2,
icfe=1, ntf=1, ntc=1,
clambda=0.5, nmropt=1,
ifsc=1, idecomp=1,
scmask=':IIA.H2',
&end
/
&wt TYPE='END'
/
LISTOUT=POUT
DISANG=RESTRAINTS.dat
system
RRES 1 6904
END
print
RES 1 6904
END
END
appear
&cntrl
ntx=5, irest=1,
ntwx=0, ntwr=20000,
ntb=2, cut=8,
nstlim=1000000, dt=0.001,
temp0=300, tempi=300, ntt=3, gamma_ln=2,
ntp=1, pres0=1, taup=2,
icfe=1, ntf=1, ntc=1,
clambda=0.5, nmropt=1,
ifsc=1, idecomp=1,
scmask=':IIP.C11,H111,H112,H113',
&end
/
&wt TYPE='END'
/
LISTOUT=POUT
DISANG=RESTRAINTS.dat
system
RES 1 6904
END
print
RES 1 6904
END
END
END
Can this be a technical problem?
Thanks Nico
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Received on Wed Feb 05 2014 - 05:30:03 PST
