Hi,
I think this issue may stem from a missing or incorrect
ATOMS_PER_MOLECULE section in the prmtop. This information is used by
cpptraj to determine where to print TER cards. You can tell cpptraj to
explicitly generate this information by specifying the 'molsearch'
keyword before loading the prmtop, e.g.:
molsearch
parm dppe.prmtop
trajin dppe.inpcrd
trajout dppe_new2.pdb pdb
That should generate proper TER cards in the PDB.
-Dan
On Fri, May 11, 2012 at 12:24 PM, Tales Yuan <yukitenkou.gmail.com> wrote:
> 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*
>> > *...*
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
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Received on Mon May 21 2012 - 04:30:04 PDT
