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 >> > >> > >> ----------------------------------------------------------------------- >> > The AMBER Mail Reflector >> > To post, send mail to amber_at_scripps.edu >> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >> > >> > >> >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to amber_at_scripps.edu >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >> > > >-- > > >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to amber_at_scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu > >

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