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On the implementation of the AMBER force field in NAMD and GROMACS

2/5/2013

4 Comments

 
The AMBER force field ff99SB-ILDN has been recently shown to perform best among other force fields. See paper by the Shaw group: "Systematic Validation of Protein Force Fields against Experimental Data"

However, AMBER is not free and does not scale very well on over 256 cores, which means that it is best to run the NAMD or GROMACS codes using the AMBER force field if you are running on more than 256 cores or do not have Amber.

However, you should carefully read and implement the directions in this document for use with NAMD (NOT the UIUC one), which should give you identical energies if followed carefully.

For use with GROMACS follow these instructions: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx or http://chemistry.csulb.edu/ffamber/

Zoe


4 Comments
Eddie
4/23/2013 10:59:16 am

Hi,
I have a pdb which has a drug and a ligand which the namd parameter/topology files cannot handle. I think amber can but I'm not completely clear on how to "implement the directions in this document." It seems to me to do what you suggest you'd need to start with amber first and then continue the amber run using namd. Is that correct? Or is there some way to use namd in cases when namd's force field is insufficient?

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    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

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