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
Received on Mon Feb 03 2014 - 04:30:02 PST
