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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Received on Wed Feb 01 2012 - 11:30:02 PST
