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.
Thanks
Jaime
________________________________________
De: case [case.biomaps.rutgers.edu]
Enviado: martes, 24 de diciembre de 2013 4:24
Para: AMBER Mailing List
Asunto: Re: [AMBER] ErrorWithLeap
On Tue, Dec 24, 2013, JAIME RUBIO MARTINEZ wrote:
>
> - I am using the last version of AmberTools
> - I am trying to solvate a big protein ( dimer ) with a big box of TIP3PBOX
> - I include the scrips and data used and also the picture of the final pdb
On additional thing to try: use ambpdb to convert the rst file into a pdb
file. Does that help? How many atoms are your final system?
....dac
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Received on Tue Dec 24 2013 - 09:30:03 PST
