Posted by Yanan Guo on April 13, 2015 at 15:28:03:
Hello Dear Molcas users,
I am running a QM/MM calculation using the molcas/tinker interface.
But the calculation just aborts when it is calculating the external potential, because the output is very long, so I just post the last part:
--- Start Module: alaska at Sat Apr 11 06:05:56 2015
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
MOLCAS executing module ALASKA with 8000 MB of memory
at 06:05:56 Sat Apr 11 2015
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
(followed is the molecular gradients calculation staff, I did not post the details)
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
MOLCAS executing module ESPF with 8000 MB of memory
at 06:26:05 Sat Apr 11 2015
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
QM/MM: found 1 MM atoms
Multipoles passed to Tinker
######################################################################
##########################################################################
### ###
### TINKER --- Software Tools for Molecular Design ###
## ##
## Version 6.2 February 2013 ##
## ##
## Copyright (c) Jay William Ponder 1990-2013 ##
### All Rights Reserved ###
### ###
##########################################################################
######################################################################
## QM/MM modifications: February 2014 ##
## Nicolas Ferre, Aix-Marseille Universite ##
## Federico Melaccio, Universita di Siena ##
This is a QM/MM calculation
24599 is defined as a QM/MM Link Atom
Tinker is called by MOLCAS
Additional Partial Charges for Specific Atoms :
Atom Charge
3488 0.0000
3489 0.0000
3490 0.0000
3473 0.5100
3474 -0.5100
3475 -0.4700
3476 0.3100
3477 0.0700
3478 0.0900
3479 -0.1800
3480 0.0900
3481 0.0900
3482 -0.1800
3483 0.0900
3484 0.0900
3485 -0.1800
3486 0.0900
3487 0.0900
3541 0.5100
3542 -0.5100
3543 -0.4700
3544 0.3100
1409 -0.1800
1410 0.0900
1411 0.0900
1412 -0.1800
1413 0.0900
1414 0.0900
1415 0.6200
1416 -0.7600
1417 -0.7600
3420 -0.1800
3421 0.0900
3422 0.0900
3423 0.6200
3424 -0.7600
3425 -0.7600
TKR2QM -- 3488 was inactive. Now active.
TKR2QM -- 3491 was inactive. Now active.
TKR2QM -- 3492 was inactive. Now active.
TKR2QM -- 3493 was inactive. Now active.
TKR2QM -- 3494 was inactive. Now active.
TKR2QM -- 3495 was inactive. Now active.
TKR2QM -- 3496 was inactive. Now active.
TKR2QM -- 3497 was inactive. Now active.
TKR2QM -- 3498 was inactive. Now active.
TKR2QM -- 3499 was inactive. Now active.
TKR2QM -- 3500 was inactive. Now active.
TKR2QM -- 3501 was inactive. Now active.
TKR2QM -- 3502 was inactive. Now active.
TKR2QM -- 3503 was inactive. Now active.
TKR2QM -- 3504 was inactive. Now active.
TKR2QM -- 3505 was inactive. Now active.
TKR2QM -- 3506 was inactive. Now active.
TKR2QM -- 3507 was inactive. Now active.
TKR2QM -- 3508 was inactive. Now active.
TKR2QM -- 3509 was inactive. Now active.
TKR2QM -- 3510 was inactive. Now active.
TKR2QM -- 3511 was inactive. Now active.
TKR2QM -- 3512 was inactive. Now active.
TKR2QM -- 3513 was inactive. Now active.
TKR2QM -- 3514 was inactive. Now active.
TKR2QM -- 3515 was inactive. Now active.
TKR2QM -- 3516 was inactive. Now active.
TKR2QM -- 3517 was inactive. Now active.
TKR2QM -- 3518 was inactive. Now active.
TKR2QM -- 3519 was inactive. Now active.
TKR2QM -- 3520 was inactive. Now active.
TKR2QM -- 3521 was inactive. Now active.
TKR2QM -- 3522 was inactive. Now active.
TKR2QM -- 3523 was inactive. Now active.
TKR2QM -- 3524 was inactive. Now active.
TKR2QM -- 3525 was inactive. Now active.
TKR2QM -- 3526 was inactive. Now active.
TKR2QM -- 3527 was inactive. Now active.
TKR2QM -- 3528 was inactive. Now active.
TKR2QM -- 3529 was inactive. Now active.
TKR2QM -- 3530 was inactive. Now active.
TKR2QM -- 3531 was inactive. Now active.
TKR2QM -- 3532 was inactive. Now active.
TKR2QM -- 3533 was inactive. Now active.
TKR2QM -- 3534 was inactive. Now active.
TKR2QM -- 3535 was inactive. Now active.
TKR2QM -- 3536 was inactive. Now active.
TKR2QM -- 3537 was inactive. Now active.
TKR2QM -- 3538 was inactive. Now active.
TKR2QM -- 3539 was inactive. Now active.
TKR2QM -- 3540 was inactive. Now active.
TKR2QM -- 24599 was inactive. Now active.
Coordinates/multipoles updated from MOLCAS
Tinker is computing the MM contribution to the QM/MM energy
and the MM contributions to the gradient
eb = 0.09197626 ua = 57.71597646 kcal/mol
ea = 0.18822492 ua = 118.11292327 kcal/mol
eid = 0.00770329 ua = 4.83388563 kcal/mol
et = 0.12702727 ua = 79.71081678 kcal/mol
ev = -0.24865851 ua = -156.03557083 kcal/mol
ec = 0.49913997 ua = 313.21505756 kcal/mol
Tinker is computing the MM electrostatic potential
Back from Tinker
MM gradients have been updated
External potential:
Atom E Fx Fy Fz Gxx Gyy Gzz Gxy Gxz Gyz
1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
2 -0.55840 0.00585 0.01205 0.01380 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
3 -0.61596 0.01429 0.03201 0.03226 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
4 -0.52687 -0.00524 0.00945 0.00475 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
5 -0.53111 -0.01905 0.00105 0.00031 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
6 -0.50513 -0.00581 0.01279 0.00439 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
7 -0.52198 -0.00620 0.01441 0.00751 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
8 -0.46992 -0.00593 0.01145 0.00167 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
9 -0.46488 -0.00475 0.00866 -0.00240 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
10 -0.44580 -0.00485 0.01076 -0.00888 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
11 -0.46890 -0.00373 0.00442 0.00179 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
12 -0.47823 -0.00715 0.01246 -0.00050 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
13 -0.44369 -0.00842 0.01267 0.00177 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
14 -0.45790 -0.01228 0.01516 0.00664 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
15 -0.40540 -0.00665 0.01299 -0.00101 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
16 -0.39387 -0.00396 0.01296 -0.00284 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
17 -0.37701 -0.00711 0.01162 -0.00156 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
18 -0.38373 -0.00924 0.01325 0.00016 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
19 -0.34806 -0.00552 0.00858 -0.00307 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
20 -0.34529 -0.00594 0.00694 -0.00078 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
21 -0.35516 -0.00625 0.00300 0.00223 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
22 -0.32680 -0.00614 0.00668 -0.00113 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
23 -0.35230 -0.00572 0.00904 -0.00069 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
24 -0.32386 -0.00419 0.00821 -0.00364 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
25 -0.32562 -0.00509 0.00823 -0.00352 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
26 -0.30098 -0.00190 0.00780 -0.00403 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
27 -0.29911 -0.00307 0.00830 -0.00568 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
28 -0.28361 -0.00013 0.00706 -0.00286 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
29 -0.26783 0.00066 0.00636 -0.00253 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
30 -0.26472 -0.00026 0.00722 -0.00154 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
31 -0.26483 0.00132 0.00740 -0.00027 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
32 -0.27658 -0.00123 0.00778 -0.00241 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
33 -0.25056 -0.00059 0.00685 -0.00059 0.00000 --- Stop Module: alaska at Sat Apr 11 06:27:00 2015 /rc= -1 (Unknown) ---
--- Module alaska spent 21 minutes and 4 seconds
Aborting..
The following is my input file:
++ --------- Input file ---------
> EXPORT MOLCAS_MOLDEN=ON
> EXPORT MOLCAS_REDUCE_PRT=NO
> EXPORT MOLCAS_PRINT=3
> FOREACH DIHEDRAL in (10.0)
&Gateway
tinker
basis
6-31g*
group
nosym
RICD
Constraint
a
DIHEDRAL C13 C8 C6 C4
Value
a
$DIHEDRAL degree
End of Constraints
>> FOREACH A in (1..1000)
&Seward
Title
QM/MM Eisomer peptide_switch
Doana
&Espf
External
Tinker
lamorok
&Rasscf
lumorb
charge
1
spin
1
nActEl
12 0 0
Inactive
78
Ras2
12
CIROOT
3 3
1 2 3
1 1 1
RlxRoot
2
>> COPY $Project.JobIph $Project.JobOld
&Mclr
THREshold
1.0e-02
&Alaska
&Slapaf
Iterations
1000
Cartesian
rHidden
10.0
>> ENDDO <<
>ENDDO
--------------------------------------------------
Any advice would be very appreciated. Thank you very much!
Best Regards
Yanan