Hi Bala..you could also use the software "Packmol" (free), with an
input file like this:
#
# A mixture of water and protein
#
tolerance 2.0
filetype pdb
output BOX.pdb
add_amber_ter
resnumbers 2 <important: otherwise tleap will complain>
structure water.pdb
number 1000 <number of water molecules will depend on the density>
inside box 0. 0. 0. 40. 40. 40. <box edges>
end structure
structure protein.pdb
number 1
inside box 0. 0. 0. 40. 40. 40.
end structure
And then use tleap/xleap with the command:
>loadpdb BOX BOX.pdb
>setbox BOX centers
>saveamberparm BOX BOX.top BOX.crdi......
Of course you need to load the prep/off files and the forcefield
(parm03, or whatever) before loading BOX.pdb
Lorenzo
Il 26 aprile 2012 15:34, francesco oteri <francesco.oteri.gmail.com> ha scritto:
> Hi bala,
> I don't know how to do in amber, but you can use the solvate module in vmd
> and then using the generated pdb in tleap
>
> Francesco
>
> Il giorno 26 aprile 2012 11:44, Bala subramanian
> <bala.biophysics.gmail.com>ha scritto:
>
>> Hi Amber users,
>> I want to create a box of 40Ang and then place the protein and water inside
>> the box. Is there any way i can do the same in xleap. While i am aware that
>> the solvent box can be create with solvateBox command, i am not sure if it
>> can create a box of fixed size.
>>
>> Do i need to play with the distance parameter in solvateBox command, so as
>> to get the box of desired size.
>>
>> Thanks,
>> Bala
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
==========================================
Lorenzo Gontrani
Research associate of CNR-ISTM (Rome Tor Vergata)
EDXD group of University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
=========================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 26 2012 - 07:00:04 PDT
