FEP alchemical

From: Amir Shamloo (ashamloo_at_stanford.edu)
Date: Fri Jul 15 2005 - 19:51:23 CDT

Hi All

I faced a problem when I wanted to generate the coordinates of
> atoms in free energy alchemical transformation using zero sum ethane
> example
> mentioned in FEP manual of NAMD .I downloaded the ethane molecule pdb
> file
> and added a
> carbon atom and 3 hydrogen atoms to the system ,but NAMD stopped
> after one step. also when I let the program guess the missing hydrogen
> atom
> coordinates this problem remained.So my main question is how to
> produce a
> pdb file containing the coordinates of alternate atoms correctly.when
> using
> common pdb files which contain the initial state coordinates ,how we
> should
> add the final state atom coordinates to that correctly.it is very
> problematic to guess final aomic positions in conjunction with the
> initial
> atomic positions.is there any program to do so?"

Thanks in advanced

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