The problem has been solved by fixing the ATOMIC_NUMBER parameters for the Zn2+ and Ca2+ ions in the prmtop file.
> On Aug 20, 2019, at 3:28 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 26 2019 - 15:00:02 PDT
