Hi Pengfei Li
Thank you for taking the time to answer me.
I have solved the problem.
Best
>Message: 8
>Date: Thu, 18 Nov 2021 10:11:38 -0600
>From: Pengfei Li <ambermailpengfei.gmail.com>
>To: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] ?MCPB? Why is the wrong file generated in
> tleap.in
>Message-ID: <CAD481B1-DF4B-42EC-A87A-20B264CAA353.gmail.com>
>Content-Type: text/plain; charset=utf-8
>
>Hi Huimin,
>
>Please check the ?add_bonded_pairs" variable in the Page 333 of the AMBER manual: https://ambermd.org/doc12/Amber21.pdf <https://ambermd.org/doc12/Amber21.pdf>.
>
>Pengfei
>
>> On Nov 8, 2021, at 5:02 AM, Huimin Tian <201921150072.mail.bnu.edu.cn> wrote:
>>
>> Here is attachment :https://pan.bnu.edu.cn/l/EnSENN
>>
>> ????Huimin Tian <201921150072.mail.bnu.edu.cn>
>> ?????2021-11-08 18:04:08
>> ????amber.ambermd.org
>> ????MCPB? Why is the wrong file generated in tleap.in
>> Dear all,
>> I use the MCPB program to process Ni-Fe hydrogenase. The active center structure of nickel iron hydrogenase includes: Metal Ni and Fe, four -CYS, two -CN(-CN1 and -CN2), and one -CO.The corresponding PDB is in the attachment. FE is connected to -CN1, -CN2 and -CO.The residue number of FE is 548?The residue number of -CN1 is 545, the residue number of -CN2 is 546, the residue number of -CO is 547. Now I have generated a tleap.in using the following command: MCPB.py -i 1YRQ.in -s 4.But I find there are some wrong bond information.Such as "bond mol.545.N1 mol.548.FE", "bond mol.546.N2 mol.548.FE", "bond mol.547.O mol.548.FE". The correct bond should be "bond mol.545.C1 mol.548.FE", ""bond mol.546.C2 mol.548.FE", "bond mol.547.C mol.548.FE".
>> Why does this error occur?
>> Are there any way to fix this issue?
>> Thanks and Regards,Tian
>>
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Received on Thu Nov 25 2021 - 23:00:02 PST
