Hi,
Try adding ions before you solvate your solute.
addions mol Na+ 0
addions mol Na+ 113
addions mol Cl- 113
solvatebox mol TIP3PBOX 12.0 0.832
On Wed, Feb 1, 2012 at 2:11 PM, TAEJIN KIM <liquidhelium4k.yahoo.com> wrote:
> Dear Amber users.
>
> I have some questions about initial locations of ion, which are placed by
> Amber11 leap.
> I am preparing MD simulation of RNA in high salt concentration (0.3M).
> I placed ions (neutral Na+ extra Na+, Cl-) around RNA with following
> procedures.
>
> $AMBERHOME/exe/xleap -s -f leaprc.ff10
>
> loadamberparams frcmod.ionsjc_tip3p
> mol=loadpdb RNA.pdb
> solvatebox mol TIP3PBOX 12.0 0.832
> addions mol Na+ 0
> addions mol Na+ 113
> addions mol Cl- 113
> savepdb mol RNA-sol.pdb
>
>
> When I checked final structure, RNA-sol.pdb, I found that some ions are
> outside of water box. I do not think this happed because of high salt
> concentration, since I could see ions outside of water box when I put
> 0.15M NaCl too.
>
> As for another test I also placed ions with
>
> mol2=loadpdb RNA.pdb
> solvatebox mol2 TIP3PBOX 12.0 0.832
> addions mol2 Na+ 113 Cl- 113
>
> and I found more weired configuration of ions which most of them located
> at the corner of water box.
>
>
> Is there any way to use leap or force filed to avoid these problems?
>
> For me, these ion configurations look wrong since ions outside of water
> box can collide to RNA by periodic boundary condition. In addition, Cl- ion
> cloud, which is placed outside of Na+ cloud may cause artificial
> electric filed.
> If someone know how to solve this problem, please let me know.
> Thank you.
>
> TJ
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>
--
Best,
InSuk Joung
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Received on Wed Feb 01 2012 - 11:30:03 PST
