Thanks Walker. I use Amber11 + AmberTools12 now. I set $AMBERHOME to
amber12 directory as the manual said, and set the amber12/bin before
amber11/bin in PATH.(Page 23)
*echo $AMBERHOME*
*/home/user/amber12*
*echo $PATH*
*/home/user/amber12/bin:/home/user/amber11/bin:/usr/local/cuda/bin:/.......*
*which tleap*
*~/amber12/bin/tleap*
I tried ptraj and ambpdb to convert pdb from inpcrd/prmtop.
*ptraj dppe.prmtop ptraj.in* (dppe_new1.pdb)
*ampbpdb -p dppe.prmtop < dppe.inpcrd > dppe_new2.pdb*
In new1 pdb, there is NO TER card in pdbfile, either lipids or water. ( I
tried a pdb including TIP3P water )
In new2 pdb, the TER cards seems good.
*PA 1*
*PE 2*
*PA 3*
*TER*
*PA 4*
*PE 5*
*PA 6*
*TER*
*...*
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Received on Fri May 11 2012 - 09:30:02 PDT
