AMBER Archive (2004)

Subject: AMBER: adding ions to nucleic acids

From: a b (asittner_at_lycos.com)
Date: Sun Feb 08 2004 - 04:47:19 CST

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_at_UMDNJ.EDU
To: amber_at_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_at_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_at_UMDNJ.EDU>
>> To: <amber_at_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
>> >
>> >
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>> 
>> 
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>
>
>-- 
>
>
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