Dear Friends,
When I added ions with addions2 and it resolved the issue.
Thanks
On Wed, Jan 6, 2016 at 11:52 PM, Himanshu Joshi <himanshuphy87.gmail.com>
wrote:
> Hello dac,
>
> Here are the list of commands I used
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> *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*
>
--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Fri Jan 08 2016 - 03:00:03 PST
