Hi Adrein,
I am not sure I understand your question fully. If your question is "is developing a new force field is the same thing as transferring a force field over from a nonamber source?" - then the answer is no. I imagine that you will have to make sure that the force field equations are the same for how the force fields were originally developed and implemented. You will probably have to understand the atom types in Amber force fields versus the ones you want to use, and convert them as necessary. You can find all of the files concerning the force fields and residue files in your $AMBERHOME/dat/leap/ directory - such as the atom types. If the force field equation is exactly the same, then you will not have to do any curve fitting to quantum data and other force field development issues. You will want to test the new force field to make sure it is performing as it did in the other programs. You may have to introduce new atom types, but I am not sure.
What will be similar (new force field versus converting an existing one) will be how Leap recognizes the force field. This will be best understood by looking at the examples on the Amber website and reading the manual. This is about the extent of my advice, since I haven't converted a force field before. Good luck.
Cheers,
Karl
----- Original Message -----
From: Adrien Delmont <adriendelmont.yahoo.com>
Date: Tuesday, July 1, 2008 10:12 am
Subject: AMBER: concerning force fields ( to Karl Kirschner )
To: amber.scripps.edu
> Hi Dear Kirschner,
> Firstly I want to thank you for all valuable information. I will
> definitely consider all of them. I want to do different force
> fields that Amber does not provide files for my sturucture.
> And I am planning to modify gaff and use TraPPE-UA and OPLS-AA
> force fields not a new force field . And you mentioned about
> an important point that developing a new force field will be
> very difficult and can take years . So are they same things?
> and also Do these operations have same procedure as you
> explained respectively. If not what are the differences between
> the two ? Could you please explain this?
> Many thanks in advance.
> Best regards,
>
> Adrien
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Received on Wed Jul 02 2008 - 06:07:41 PDT
