That is very strange.
Can you try looking at your prmtop with parmed and see what amber really
thinks that atom is?
the atom name "
\00\00
" leds me to believe there is something else wrong, not the QM/MM
adrian
On 7/12/16 11:11 AM, Allen Zou wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jul 12 2016 - 08:30:03 PDT
