On Tue, Dec 24, 2013 at 12:14 PM, JAIME RUBIO MARTINEZ
<jaime.rubio.ub.edu>wrote:
>
> Hello,
>
> Thank you for your help !!!
>
> Effectively the problem seems to be related to the pdb 'limit' of 100000
> atoms.
>
> - I have 393924 atoms and 126325 resudues.
> - leap.log shows no errors.
> - The .pdb from leap has numbers > 100000.
>
> - If I use ambpdb to transform .rst from leap to pdb: it works nicely !
> - If I use .rst + .top + VMD : it works nicely !
>
> Also,
> - If I use .rst + .top from leap and run ptraj: the new . pdb works
> nicely !
>
> Thus it seems a problem realated to the SavePdb command in Leap.
>
Yes. Specifically, ptraj (and ambpdb, I believe) cycles atom numbers
(that is, the atom number goes from 99,999 to 0) to avoid overflowing the
width of the atom number field in the PDB file (and likewise with residues,
although I believe that turnover is 10,000 instead of 100,000).
This is a known problem with tleap-generated PDB files, although I'm unsure
if it has been fixed or not.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 24 2013 - 10:30:02 PST
