> i need to again save the topology file which creates another problem
because G3 molecule comprises of three residues and bonds between those
residues are not connected now.
Did you break those bonds? Were they ever there in the first place? This
seems unrelated to your other issues. Do not trust viewers to show you
the bonds unless they read the prmtop.
> So to avoid this i have added 80 ions of BMI but then minimisation of
solvent gives the error.
How did you add the BMI?
> minimisation of solvent gives the error.
Sounds like you have homework to do.
Bill
On 12/11/17 4:20 AM, Shilpa Gupta wrote:
> I have generated ionicbox with 300 BMI cations and 300 Chloride anions. Now
> i have solvated the molecule using following scritp
> source leaprc.gaff
> loadamberparams frcmod.bmi
> G3=loadmol2 USER.mol2
> BMI = loadmol2 bmi.mol2
> Cl = loadmol2 cl.mol2
> ionicbox=loadpdb ionicbox.pdb
> solvatebox G3 ionicbox 10.0
> saveamberparm G3 ionicbox.prmtop ionicbox.inpcrd
>
> By this method G3 molecule solvated by 200 BMI(cations) and 280 Cl(anions)
> and if i am deleting the extra chloride ions then i need to again save the
> topology file which creates another problem because G3 molecule comprises
> of three residues and bonds between those residues are not connected now.
> So to avoid this i have added 80 ions of BMI but then minimisation of
> solvent gives the error.
>
> On 11 December 2017 at 12:12, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> 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
>>>>> _______________________________________________
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Received on Mon Dec 11 2017 - 05:30:02 PST
