I use cpptraj but it also don't print TER cards.
*cpptraj -i ptraj.in -p dppe.prmtop*
2012/5/12 Daniel Roe <daniel.r.roe.gmail.com>
> 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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>
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Received on Fri May 11 2012 - 09:30:03 PDT
