Hi Amber experts,
I wanted to study a heme-contained protein using QMMM-MD with
Amber/Gaussian. QM region include heme, a HID residue and my ligand which
contained 135 atoms. When I do minimization using QMMM preference, it seems
there is a problem in my QM/MM simulation, and I find that QMMM can't
recognize Fe atom (atom number: 6387) as listed below:
Here is the input file:
Minimization of the entire molecular system QMMM
&cntrl
imin=1, maxcyc=3000, ncyc=1500,
cut=8.0, ntb=1, ntc=2, ntf=2,
ntpr=500,
ntr=0,
ifqnt=1
/
&qmmm
qmmask=':346,404,405',
qmcharge=-2,
qm_theory='EXTERN',
qm_ewald=0
/
&gau
basis = '6-31G**',
method = 'B3LYP',
num_threads = 2,
mem = '1GB',
/
.......................
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 5468 N -4.6859 -1.3742 -7.2613
QMMM: 2 5469 H -5.0284 -0.4962 -7.6245
QMMM: 3 5470 C -4.1202 -1.3711 -5.9212
QMMM: 4 5471 H -3.0443 -1.5274 -5.9991
QMMM: 5 5472 C -4.3737 -0.0047 -5.2884
QMMM: 6 5473 H -4.0340 0.8126 -5.9246
QMMM: 7 5474 H -5.4437 0.0921 -5.1047
QMMM: 8 5475 C -3.7352 0.1311 -3.9601
QMMM: 9 5476 N -4.4233 -0.0120 -2.7757
QMMM: 10 5477 H -5.4131 -0.1710 -2.6526
QMMM: 11 5478 C -3.5569 0.1585 -1.7894
QMMM: 12 5479 H -3.7931 0.1401 -0.7357
QMMM: 13 5480 N -2.3519 0.3235 -2.3100
QMMM: 14 5481 C -2.4201 0.3643 -3.6742
QMMM: 15 5482 H -1.5609 0.5070 -4.3127
QMMM: 16 5483 C -4.6947 -2.5006 -5.0521
QMMM: 17 5484 O -3.9446 -3.2113 -4.3947
QMMM: 18 6387 \00\00 -0.9709 1.2345 -0.9488
QMMM: 19 6388 N -1.9485 0.5044 0.6766
QMMM: 20 6389 C -2.9451 1.1482 1.3738
QMMM: 21 6390 C -3.4130 0.2792 2.4237
QMMM: 22 6391 C -4.5355 0.5456 3.3809
QMMM: 23 6392 H -4.4181 -0.1845 4.1817
QMMM: 24 6393 H -5.4809 0.3306 2.8829
QMMM: 25 6394 C -4.5529 1.9284 4.0508
QMMM: 26 6395 H -5.5398 2.1064 4.4779
...................
>>> Running calculations with Gaussian <<<
| &gau
| method = B3LYP
| basis = 6-31G**
| guess = read
| mem = 1GB
| scf_conv = 8
| ntpr = 500
| num_threads = 2
| debug = 0
| dipole = F
| use_template = F
| /
| Program g09 found!
| Executable location: /home/zou/g09//g09
----------------------------------------------------------------------------
----
4. RESULTS
----------------------------------------------------------------------------
----
SANDER BOMB in subroutine get_gau_forces (qm2_extern_gau_module)
Error with system call (executing Gaussian)
Will quit now.
The terminal of Ubuntu showed the message:
>:~home $ sander -O -i min2.in -p complex_wt.prmtop -c complex_wt_min1.rst
-ref complex_wt_min1.rst -r complex_wt_min2.rst -o complex_wt_min2.out
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx 00002b72550024f7
rdx 0000000000000b8b, rsp 00007ffe0208f9f8, rbp 00007ffe0208ff70
rsi 000000000000000b, rdi 0000000000000b8b, r8 00002b7255393970
r9 00002b72548c2340, r10 0000000000000228, r11 0000000000000202
r12 0000000000000000, r13 0000000000000000, r14 00007ffe0208ffb8
r15 00000000000003e6
--- traceback not available
Aborted (core dumped)
Error: segmentation violation
rax 0000000000000000, rbx 00000000006933c8, rcx 00002b6b6809a4f7
rdx 0000000000000b8f, rsp 00007fff37d3f168, rbp 00007fff37d3f1c0
rsi 000000000000000b, rdi 0000000000000b8f, r8 00002b6b6842b970
r9 00002b6b6795a340, r10 0000000000000228, r11 0000000000000202
r12 0000000000000000, r13 0000000000000002, r14 0000000000000000
r15 0000000000000000
--- traceback not available
Aborted (core dumped)
Sincerely,
Allen Zou
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Received on Tue Jul 12 2016 - 08:30:02 PDT
