From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jul 20 2011 - 10:30:02 CDT

That is indeed the case (Ed sent me a copy of his files).

Cheers,
Leo

On Wed, Jul 20, 2011 at 5:20 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Are any of the atom types longer than four characters?  The latest CHARMM
> forcefields have six-character types, which technically breaks the PSF
> format and causes various issues like the one you describe, although NAMD
> can still handle it.
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Leonardo Trabuco
> Sent: Wednesday, July 20, 2011 9:41 AM
> To: Edward Lyman
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: autoionize adds too many ions
>
> Hi Ed,
>
> Could you please send me a copy of your system off-list? I'll try to
> track down the problem.
>
> Thanks,
> Leo
>
> On Fri, Jul 15, 2011 at 9:34 PM, Edward Lyman <edward.lyman_at_gmail.com>
> wrote:
>> Hi all,
>>
>> I have built a micelle with 100 or so neutral detergent molecules. I
>> have checked the charge on each detergent molecule, it is ~10**-16e. I
>> built a water box around it, and then tried to use the autoionize
>> plugin to add 0.150 mM NaCl. After adding ions, the plugin complained
>> that the system has a non integer charge. For some reason 394 Cl ions
>> were added, and 27 Na. Any thoughts on what I'm doing wrong? Been
>> banging my head on the wall for a day over it...
>>
>> Best,
>> Ed
>>
>> ps --- I am using vmd 1.9
>>
>>
>
>
>
> --
> Leonardo Trabuco, Postdoctoral fellow (Russell group)
> CellNetworks, University of Heidelberg, Germany
> http://www.russelllab.org/people/leo/
>
>

-- 
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/