Just a thought:
Have you tried saving your pdb file into two separate pdb files of <
1000000 each (potentially with renumbering through a script), and then
reading each of these in separately into tleap, before combining them?
part1 = loadpdb part1.pdb
part2 = loadpdb part2.pdb
mol = combine {part1 part2}
HTH,
Marc
On 12 August 2016 at 08:53, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> I have a biphasic system with > 1000000 atoms and the obvious problem is
> pdb files can support numbering upto 99,999 atoms. Is there a way to load
> files in tleap other than pdb or mol2 format?
>
> When I save pdb file in chimera, it will save atoms > 99999 as ****. AMBER
> will complain about duplicate numbering. Programs like Discovery studio
> don't even allow saving such a big pdb file. Most programs will prefer
> mmCif format. How do I get around working with this issue in tleap?
>
> Regards,
> Neha
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Received on Fri Aug 12 2016 - 01:30:02 PDT
