Cpptraj should print TER cards in PDB files; it will take the same input as ptraj.
-Dan
On May 11, 2012, at 12:11 PM, Tales Yuan <yukitenkou.gmail.com> wrote:
> 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
