Dear Zhou,
I am sending this message to the AMBER mailing list since this is best place for these types of questions.
I believe what you say is fine, that is you can edit the leaprc files to specify RNA instead of DNA. For a pure RNA simulation using leaprc.RNA.ff99 vs (RNA modded) leaprc.ff99SB. If you are mixing protein and RNA and want to use FF99SB for the protein then yes you need to modify the leaprc.ff99SB - although you are probably better creating your own copy called leaprc.RNA.ff99SB so you don't overwrite the original and then later forget that it was modified. If you are mixing DNA and RNA then you will need to modify the PDB file to specify which residue is which - by manually changing the residue name to RG5, RA5 etc etc. You could of course also do this with a pdb containing just RNA if you don't want to modify the leaprc files.
Good luck,
Ross
From: zgong.hust [mailto:zgong.hust.gmail.com]
Sent: Wednesday, January 07, 2009 2:39 AM
To: Ross Walker
Subject: Re: RE: amber force filed for RNA
Dear sir:
I have check the differences between leaprc.rna.ff99 and leaprc.ff99 carefully. I found that the "leaprc.ff99" assumes that any unspecified nucleic acids are DNA, while the "leaprc.rna.ff99" assumes that any unspecified nucleic acids are RNA. The differences between them are the addpdbresmap and addpdbatommap in the leaprc files. If I change the addpdbresmap and addpdbatommap in the leaprc files. I can use the leaprc.ff99 correctly, I can also use change them in the other force filed such as ff96,ff03. Whether can I do it like this?
2009-01-07
_____
zgong.hust
_____
发件人： Ross Walker
发送时间： 2009-01-07 10:58:04
收件人： 'zgong.hust'
抄送：
主题： RE: amber force filed for RNA
Hi Zhou,
I haven't tried this myself so you may want to post the question to the amber mailing list. However, I believe that the leaprc.ff99SB etc files are setup just to support DNA. I believe that if you need a protein mixed with RNA then you need to load the leaprc.ff99SB and then source the leaprc.rna.ff99 file. I think this will then override the DNA settings. As I say I haven't tried this myself though but give it a try and see. Also make sure you have TER cards in the correct places like it describes in the tutorial.
Good luck,
Ross
From: zgong.hust [mailto:zgong.hust.gmail.com]
Sent: Friday, December 26, 2008 4:02 AM
To: Ross Walker
Subject: amber force filed for RNA
Dear sir:
I would like to do the molecular dynamics of RNA using amber. When I use the force field like leaprc.rna.ff02, leaprc.rna.ff99, leaprc.rna.ff98, It is right, and I could get the prmtop and inpcrd files.
However, when I use the force field such as ff03,ff96,or ff99, the leap gave the information like this:
Unknown residue: U number: 2 type: Nonterminal
Unknown residue: U number: 3 type: Nonterminal
Created a new atom named: P within residue: .R<DG5 31>
Created a new atom named: O1P within residue: .R<DG5 31>
Created a new atom named: O2P within residue: .R<DG5 31>
Created a new atom named: O2* within residue: .R<DG5 31>
Created a new atom named: O2* within residue: .R<DC 32>
Creating new UNIT for residue: U sequence: 33
One sided connection. Residue: missing connect0 atom.
Created a new atom named: P within residue: .R<U 33>
Created a new atom named: O1P within residue: .R<U 33>
Created a new atom named: O2P within residue: .R<U 33>
Created a new atom named: O5* within residue: .R<U 33>
Created a new atom named: C5* within residue: .R<U 33>
In your AMBER8 tutorial about DNA, you can use ff99, Why didn't I use it for RNA?
Whether these force field are not suitable for RNA?
Thank you
2008-12-26
_____
zgong.hust
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Received on Fri Jan 09 2009 - 01:10:53 PST
