Hi Geng,
Have you checked whether the ATOMIC_NUMBER parameters of the Zn2+ and Ca2+ ions are correct?
Pengfei
> On Aug 19, 2019, at 4:51 AM, 东庚 <gdong.stu.edu.cn> wrote:
>
> 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
>
> ________________________________
> 发件人: 东庚 <gdong.stu.edu.cn>
> 发送时间: 2019年8月18日 11:20:03
> 收件人: amber.ambermd.org <amber.ambermd.org>
> 主题: 答复: 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
>
> ________________________________
> 发件人: 东庚 <gdong.stu.edu.cn>
> 发送时间: 2019年8月17日 11:10:11
> 收件人: amber.ambermd.org <amber.ambermd.org>
> 主题: 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
> ________________________________
> 发件人: 东庚
> 发送时间: 2019年8月15日 15:20:20
> 收件人: amber.ambermd.org <amber.ambermd.org>
> 主题: 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 Tue Aug 20 2019 - 12:30:02 PDT
