Hi,
For my problem, I found that the program does not run with qmmm_module.F90.
For znic ion, the program gave a wrong print of QMMM: 55 6683 ^@^@ -1.0230 7.0360 -32.8160 ,
for Ca ion, carbon was gave, i.e. QMMM: 55 6682 C 18.8090 3.9170 -30.0640
How can I solve this problem?
Best,
Geng
________________________________
·¢¼þÈË: ¶«¸ý <gdong.stu.edu.cn>
·¢ËÍʱ¼ä: 2019Äê8ÔÂ18ÈÕ 11:20:03
ÊÕ¼þÈË: amber.ambermd.org <amber.ambermd.org>
Ö÷Ìâ: ´ð¸´: probelm -- QMMM-MD with ZN£¨Znic atom£©in QM region
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
________________________________
·¢¼þÈË: ¶«¸ý <gdong.stu.edu.cn>
·¢ËÍʱ¼ä: 2019Äê8ÔÂ17ÈÕ 11:10:11
ÊÕ¼þÈË: amber.ambermd.org <amber.ambermd.org>
Ö÷Ìâ: probelm -- QMMM-MD with ZN£¨Znic atom£©in 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
________________________________
·¢¼þÈË: ¶«¸ý
·¢ËÍʱ¼ä: 2019Äê8ÔÂ15ÈÕ 15:20:20
ÊÕ¼þÈË: amber.ambermd.org <amber.ambermd.org>
Ö÷Ìâ: probelm -- QMMM-MD with ZN£¨Znic atom£©in 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 Mon Aug 19 2019 - 02:00:02 PDT
