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?
Also the result does not change by excluding the RRES card.
Kind regards
Nico Schackert
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 03 2014 - 04:00:02 PST
