Hello dac,
Here are the list of commands I used
*source leaprc.lipid14source leaprc.ff14SBloadamberparams
frcmod.ionsjc_tip3pp = loadpdb ../new1_combined.pdbsolvateBox p TIP3PBOX {0
0 15}#source remove_badwaters.leapaddions p MG 1308addions p Cl- 0check
psaveoff p systemA.libsavepdb p
systemA.pdb
saveamberparm p systemA.prmtop systemA.inpcrd*
Although, I didn't try addions2/ addIonsRand earlier,
I am trying them now and update you with the proceedings.
Thanks
~
On Wed, Jan 6, 2016 at 6:23 PM, David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jan 06, 2016, Himanshu Joshi wrote:
>
> > I am adding ions to my system after solvating it with TIP3PBOX in xleap.
> > After adding Mg ions, if I add Cl- ions to built a system with desired
> > molarity,
> > xleap is placing the ions out of the periodic box set up by previous
> > solvation command.
>
> Can you give the exact list of commands you used? Do you get
> different/better
> behavior if you use addIons2 or addIonsRand?
>
> ...dac
>
>
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--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Wed Jan 06 2016 - 10:30:03 PST
