Hi Everyone,
My RNA molecule has three dimensions of 200, 160, 180 Angstroms, I did the steps as shown below. From the final pdb with waters, the water box contains only a portion of the molecule, and a long pole consisting of only H atoms. Due to the email size limitation, I can't attach an image to show the pdb. When the size of an RNA molecule is reduced to somewhere around 100 Angstroms, I did not find such problems
/usr/local/amber16/bin/tleap
source /usr/local/amber16/dat/leap/cmd/oldff/leaprc.ff14SB
loadamberparams /usr/local/amber16/dat/leap/parm/frcmod.ions234lm_1264_tip3p
x=loadpdb mol.pdb
addions x Na+ 0
solvateBox x TIP3PBOX 10.0 (or solvateoct x TIP3PBOX 10.0))
savepdb x x.pdb
Could anyone kindly tell me what is the problem. Does solvateBox work for limited size of an RNA?
Thank you!
Wen
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Received on Thu Apr 13 2017 - 07:30:02 PDT
