Re: [AMBER] Force Field for DNA-Protein complex

From: David A Case <>
Date: Tue, 30 Jul 2013 10:15:50 -0400

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.


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Received on Tue Jul 30 2013 - 07:30:02 PDT
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