Hi Muthukumaran,
Yeah. MCPB.py can handle such a system and let me know if you need any help.
-Pengfei
> On Apr 17, 2019, at 1:36 AM, Muthukumaran Rajagopalan <kumaran.bicpu.edu.in> wrote:
>
> Dear Pengfei,
>
> Thank you for the suggestions.
>
> I have mercury chloride connected via co-ordinate bond to chemical compound. Your suggestions will be helpful.
>
> On 04/17/19 07:03 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>>
>> Hi Muthukumaran,
>>
>> You can use MCPB.py to parameterize the metal site: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
>>
>> Hope it helps,
>> Pengfei
>>
>>> On Apr 16, 2019, at 1:24 PM, Muthukumaran Rajagopalan <kumaran.bicpu.edu.in> wrote:
>>>
>>> Dear AMBER users,
>>>
>>> (i) I am trying to generate force field parameters for Mercury chloride connected via co-ordinate bond to amino acid. Antechamber recognises this coordinate bond as non-bonded. The command used is antechamber -i file.mol2 -fi mol2 -o min_sqm.mol2 -fo mol2 -c bcc -j5 -dr no. But parmchk is not able to define the bond and angle parameters correctly. how to rectify it?
>>>
>>> (ii) Next, I tried to generate force field parameters by RESP method. The compound was optimised using Gaussian (Mp2; lanl2dz). The force constants are derived from frequency calculations. Can these frequencies used as force constants? Or any other alternatives to proceed?
>>>
>>> Any suggestions and pointers regarding this would be very helpful.
>>>
>>> Thanks in advance.
>>>
>>> Muthukumaran Rajagopalan
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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> --
> with regards
>
> R. Muthukumaran
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Received on Fri Apr 19 2019 - 09:00:02 PDT
