You could do the solvation, then add the balancing ions manually, e.g.
by replacing solvent, editing the pdb (delete all but one atom of a
solvent residue, and change its residue/atom names to the desired ion).
Then equilibrate to forget your sins, and let the science begin! :-)
Bill
On 12/10/17 10:09 PM, Shilpa Gupta wrote:
> Since the solvent pdb has cations as well anions therefore with loadpdb
> command solvent is being added but in unequal number (randomly), and i want
> equal number of cations and anions.
>
>
> On 11 December 2017 at 11:35, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> <ignore>You have to manually re-type the pdb file for it to work
>> :-)</ignore>
>>
>> Try loading the box with loadpdb, then use it like you'd use any other box.
>>
>> Bill
>>
>>
>> On 12/10/17 8:37 PM, Shilpa Gupta wrote:
>>> Dear Amber Users,
>>> I want to know that how can i solvate the molecule in amber, if the
>> solvent
>>> box i have generated using packmol rather than creating the whole
>> solvated
>>> system in packmol.
>>>
>>>
>>> Shilpa
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 10 2017 - 23:00:03 PST
