[AMBER] : probelm -- QMMM-MD with ZNZnic atomin QM region

From: <gdong.stu.edu.cn>
Date: Sun, 18 Aug 2019 02:20:03 +0000

Hi Pengfei,

I have checked the parmtop file, and the name of zinc ion is Zn

O CA Zn Na+ Na+ Na+ Na+ Na+ Na+ Na+ O H1 H2 O H1 H2 O H1 H2 O
and its mass is
 0.16000000E+02 0.40100000E+02 0.65400000E+02 0.22990000E+02 0.22990000E+02


If I run my simulation without the Znic ions, then amber worked fine. It seems that the sander/sander.MPI did not use the program of qmmm_module.F90. Is it possible to compile just the qmmm module with all needed programs in amber? Or how can I check that I have compiled the qmmm part with all the modules correctly?

Best,

Geng

________________________________
: <gdong.stu.edu.cn>
ʱ: 2019817 11:10:11
ռ: amber.ambermd.org <amber.ambermd.org>
: probelm -- QMMM-MD with ZNZnic atomin QM region

Hi,
I am a AMBER user in Shantou University Medical College. I want to run the QMMM-MD calcualtions with gaussian program for QM. In my calculation, the ZN(znic atom) was included in the QM region. However, I got a problem that the ZN(znic atom) cannot be identifiled by sander/sander.MPI), which results in a crash of gaussian calculation. The problem in sander output file is shown as following
  QMMM: 53 5515 C 2.9660 8.2120 -35.0540
  QMMM: 54 5516 H 3.3310 9.1910 -35.3270
  QMMM: 55 6683 ^@^@ -1.0230 7.0360 -32.8160
  QMMM: 56 *H -7.8917 11.8993 -31.4762
  QMMM: 57 *H -7.3375 7.5579 -32.8057
the ^@^@ should be ZN.

which leads to a probelm in gaussian input file is

H 3.3310000000000000 9.1910000000000007 -35.3269999999999982
^.^. -1.0229999999999999 7.0359999999999996 -32.8160000000000025
H -7.8917239096519642 11.8993434579117849 -31.4761545477141134
H -7.3375174660172018 7.5578871628299602 -32.8057071544340744

I attached all the input and output files in the mail. How can I solve this problem?
Thank you.
Best,
Geng
________________________________
:
ʱ: 2019815 15:20:20
ռ: amber.ambermd.org <amber.ambermd.org>
: probelm -- QMMM-MD with ZNZnic atomin QM region



Hi,

I am a AMBER user in Shantou University Medical College. I want to run the QMMM-MD calcualtions with gaussian program for QM. In my calculation, the ZN(znic atom) was included in the QM region. However, I got a problem that the ZN(znic atom) cannot be identifiled by sander/sander.MPI), which results in a crash of gaussian calculation. The problem in sander output file is shown as following

  QMMM: 53 5515 C 2.9660 8.2120 -35.0540
  QMMM: 54 5516 H 3.3310 9.1910 -35.3270
  QMMM: 55 6683 ^@^@ -1.0230 7.0360 -32.8160
  QMMM: 56 *H -7.8917 11.8993 -31.4762
  QMMM: 57 *H -7.3375 7.5579 -32.8057
the ^.^. should be ZN.

which leads to a probelm in gaussian input file is

H 3.3310000000000000 9.1910000000000007 -35.3269999999999982
^.^. -1.0229999999999999 7.0359999999999996 -32.8160000000000025
H -7.8917239096519642 11.8993434579117849 -31.4761545477141134
H -7.3375174660172018 7.5578871628299602 -32.8057071544340744

I attached all the input and output files in the mail. How to solve this problem?
Thank you.
Best,
Geng

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Received on Sat Aug 17 2019 - 19:30:02 PDT
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