Re: [AMBER] ErrorWithLeap

Date: Tue, 24 Dec 2013 17:14:55 +0000


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 !

- 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.



De: case []
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?


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Received on Tue Dec 24 2013 - 09:30:03 PST
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