[AMBER] QM/MM problems with Amber/Gaussian

From: Allen Zou <zycz138.126.com>
Date: Tue, 12 Jul 2016 23:11:25 +0800

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
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