Well usually I dod it with the standard Leap procedure,
addions unit Na+ 0
or
addions unit K+ 0
Vlad
a b wrote:
>hi there,
>i would like to minimize some nucleic acid structure (together w/ a protein). the na structure is of course highly charged and will "explode" upon minimization.
>i order to stabilize it , i'd like to add counter ions in some "smart" procedure. (i'm afraid that the ions will "over-stabilize" wrong structures by creating many local energy minima).
>so, how do i do it?
>thanks,
>t.
>--
>
>--------- Original Message ---------
>
>DATE: Tue, 03 Feb 2004 20:39:44
>From: aini.UMDNJ.EDU
>To: amber.scripps.edu
>Cc:
>
>
>
>>Dear Dr. Simmerling,
>>
>> Thank you for your answer. However it is not clear for me. Can you give
>>more details? I tried to search through amber archives and found out
>>nothing because of lack of proper keywords.
>>Thank you very much!
>>
>>aini
>>
>>Quoting Carlos Simmerling <carlos.csb.sunysb.edu>:
>>
>>
>>
>>>if you are using parm94 or parm99, formation
>>>of helix may indicate a force field problem.
>>>this has been documented in the literature, check the
>>>amber archives.
>>>carlos
>>>
>>>----- Original Message -----
>>>From: <aini.UMDNJ.EDU>
>>>To: <amber.scripps.edu>
>>>Sent: Tuesday, February 03, 2004 6:49 PM
>>>Subject: AMBER: A general question
>>>
>>>
>>>
>>>
>>>>Dear Ambers,
>>>>
>>>> I have a general question about MD simulation. Is it possible to
>>>>
>>>>
>>>observe
>>>
>>>
>>>>secondary structure formation (e.g. helix) from a loop during the MD
>>>>simulation? I am running a simulation on protein-ligand complex. I
>>>>
>>>>
>>>found
>>>
>>>
>>>>out a extra short helix formed in our average structure after 500 ps
>>>>
>>>>
>>>GBSA
>>>
>>>
>>>>simulation.
>>>>
>>>>Thank you very much!
>>>>aini
>>>>
>>>>
>>>>
>>>>
>>>-----------------------------------------------------------------------
>>>
>>>
>>>>The AMBER Mail Reflector
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>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>--
>>
>>
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>>
>>
>
>
>
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--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
home tel: ++49-551-9963204
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Received on Sun Feb 08 2004 - 12:53:00 PST
