Dear Prof. Case,
Thanks for kind reply.
In the AMBERTools12 manual, I noted that ff12SB using the following force fields:
Protein --> ff99SB + new backbone and side chain torsions
DNA --> ff99 + Barcelona backbone torsion modifications
Is "ff99 + Barcelona backbone torsion modifications" same as f99bsc0 for DNA?
Would you mind to let us know the references paper for these new force fields? Is ff12SB only available for AMBER12? Can we use ff12SB in AMBER 10?
Where can we download the AMBER10 and ambertools10(if any?) manuals?
Best regards,
Catherine
> Date: Tue, 30 Jul 2013 10:15:50 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Force Field for DNA-Protein complex
>
> On Tue, Jul 30, 2013, Catein Catherine wrote:
>
> > I am using AMBER10 and AMBER12.
> > I prepared the prmtop and inpcrd files using leaprc.ff99bsc0 command.
> > What is the name of force fields used for DNA and Protein respectively.
> > I believe ff99SB was used for protein, f99bsc0 was used for nucleic
> > acids. Am I correct?
>
> This is correct: you can read the comments in the leaprc.ff99sbc0 file, or
> consult the section "Choosing a force field" in the AmberTools Manual.
>
> > Can I read the force field information from the inpcrd or prmtop files
> > directly?
> > Is it the right force field to be used for DNA-Protein complex?
>
> The protein force field has been updated (ff99SB dates from 2006): see the
> Manual for details. The most recent recommended leaprc file is leaprc.ff12SB.
>
> ...regards...dac
>
>
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Received on Tue Jul 30 2013 - 08:30:03 PDT
