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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