AMBER Archive (2002)

Subject: Re: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 01 2002 - 07:51:26 CST

On Fri, Nov 01, 2002, Pascal Bonnet wrote:
>
> Why does LEAP change the topological type of some atoms?
> I would like to conserve the topological type in the prep file.

(1) Why do you want to do this? Amber makes no use of the tree classification
information in the prmtop file. If you need it for other programs, you could
hand-edit the prmtop to put your classification in there.

(2) Are the two trees both correct (yours and LEaP's)?

>
> question 2) there are no parameters for c-ct-ca or c2-ct-ca in the gaff
> force field.

Have you used parmchk? This is what is intended for people to use with
missing parameters in gaff.

..good luck...dac 

-- 

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