AmberTools 16 is the recommend package for ParmEd and cpptraj in
particular, but other programs in general (ParmEd and cpptraj have
undergone many improvements since AmberTools 15 was released).
fixatomorder in cpptraj should also work.
HTH,
Jason
On Tue, Jun 7, 2016 at 8:00 AM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> Thank you both for your suggestions.
>
> I tried to add TER cards and create prmtop/inpcrd files, but if I check
> them with parmed.py, the same warning appears.
> Is that a 14at15 bug, to recommend the latest version of AmberTools?
> Can any fixatomorder in cpptraj, fix it?
>
> Cheers,
> Damiano
>
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> Sent: 07 June 2016 09:14
> To: AMBER Mailing List
> Subject: Re: [AMBER] setMolecules failed
>
> On Mon, Jun 06, 2016, Damiano Spadoni wrote:
> >
> > I used the .pdb file of a protein surrounded by 300 oxygen molecules
> > to feed in xleap,
>
> Does the PDB file have TER cards between each of the oxygen molecules?
> If not, give that a try.
>
> ....dac
>
>
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Received on Tue Jun 07 2016 - 08:00:13 PDT
