Hi Atul,
I've never used packmol.
Bill
On 10/12/17 3:34 AM, ATUL KUMAR wrote:
> Thank you Bill,
> Actually I tried using packmol but I am not sure about the way I have
> contracted 6M GDMCl box.
> So this is basically how I have done it.
> (i) i created a box of padding distance of 15ang around my protein(lets say
> the volume of box is V and it has W number of waters) then I calculated
> number of GDM (lets say the number is X ) and Cl (lets say Y number of Cl)
> molecules needed to make this box of 6M GDMCL concentration.
> (ii) in the next step I calculated how many water molecules will be
> replaced when I will add X GDM and Y Cl chlorine molecules lets say X GDM
> replaces X1 number of water and Y Cl- ion replaces Y1 number of water
> molecule.
> (iii) in the last step i packed a box of volume V with X number of GMD, Y
> number of Cl, W-X1-Y1 number of water and protein.
>
> Is this correct or I need to do something else???
>
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
>
> On Thu, Oct 12, 2017 at 3:32 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Packmol might be useful to pack your molecules into a pdb for
>> leap/amber. Unless someone has published a guanidinium model, look into
>> tutorials on defining new molecules/residues.
>>
>> Bill
>>
>>
>> On 10/12/17 2:58 AM, ATUL KUMAR wrote:
>>> Dear Amber Users,
>>> I want to make a simulation box of 6M GDM (guanidinium Chloride)
>> simulation
>>> box around a protein? Can someone help me with it?
>>> Thank You
>>>
>>>
>>> *Atul Kuamr jaiswal*
>>> Research Scholar
>>> School of Computational and Integrative Sciences
>>> Centre for Computational Biology and Bioinformatics (CCBB)
>>> JNU,New Delhi
>>> India.
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Oct 12 2017 - 12:30:02 PDT
