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.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Oct 12 2017 - 04:00:02 PDT
