Re: AMBER: read pdb back to xleap after solvation of chloroform

From: Furse, Kristina Elisabet <>
Date: Fri, 20 May 2005 16:20:55 -0500

If I understand correctly what you are trying to do, then I don't think you
really need to go back through leap with pdb's. Sounds like you want to take 500
frames from a trajectory and energy minimize them, then compare the energies. If
that is the case, you can read the trajectory into ptraj, and output the frames
as restart files (.rst) and use these directly with your original parmtop file
to run the minimizations. Of course, this does not resolve the leap chloroform
issue, and might not be what you meant to do at all!

Good luck,

Quoting chaiann ng <>:

> Dear DAV,
> What i am trying to do is re-minimized the 500 strucutres with explicit
> solvent from dynamic, and select the 20 lowest energy structures. So I use
> tleap to read in all the parameter, force field, and finally my txt file
> that contain
> vm0000 = loadpdb split0000.pdb
> saveamberparm vm0000 vm0000.prmtop vm0000.inpcrd
> etc...
> This scheme is working with water, I am just wondering what is missing in
> chloforom?
> You can try it by just read in a normal molecule and solvate it with
> chcl3box, then save as pdb.
> Now you read in that pdb again in xleap after you load everything, you will
> get the same sort of error.
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse.Vanderbilt.Edu
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Received on Mon May 23 2005 - 09:53:01 PDT
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