[AMBER] Prevent tleap to rearrange my ions?

From: chicago.ecnu <chicago.ecnu.gmail.com>
Date: Sun, 26 Jun 2011 18:18:13 +0800

Dear Amber users,


  I want to do some analysis of the trajectory file generated by Gromacs4.5 with ptraj of Amber.
 System information: Protein + water + ions . PBC . Amber99SB force field.

 Frirst, I wrote a script to convert gromacs md.xtc file into amber md.crd .
 Second, I need to prepare a prmtop file for ptraj.
 The problem comes. Unlike Amber, Ions were added at the end of the pdb file in Gromacs.
 When I reload the pdb file generated by Gromacs into tleap, ions were rearranged after protein.
 I even try to seperate ions out of the protein+water. And then combine them. That still can't work.

 Is there anyway i can try to prevent tleap to rearrange my ions ? (Is there a command like "clearpdbresmap"? )


Many Thanks.

Sincerely,

Chicago Ji.
 


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Received on Sun Jun 26 2011 - 03:30:03 PDT
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