From: Win Liu (mdsimulate_at_gmail.com)
Date: Sun Mar 31 2013 - 16:24:38 CDT

Chris,
I am using VMD 1.9.1 version. Thanks a lot for the suggestion, I will try
1.9.2 alpha and let you know.

Wenhao

2013/3/31 Christopher Mayne <mayne_at_ks.uiuc.edu>

> Wenhao,
>
> Searching back through my inbox this error came up a couple of times quite
> a while ago. Upgrading to the latest version of ffTK seemed to fix it for
> some users, although I'm not sure we ever identified exactly what was
> causing the error.
>
> What version of VMD are you using? I would suggest downloading the latest
> 1.9.2 alpha build from BioCoRE.
>
> Regards,
> Christopher
>
> On Mar 31, 2013, at 2:24 PM, Win Liu wrote:
>
> Hi Chris,
> Thanks for your suggestion. But I tried cd to a permission allowed
> directory, but this issue occurred again. And I tried file delete
> base-wat.pdb command in that directory and this command worked. So I really
> don't how this error come out and how to fix it.
>
> Wenhao
>
> 2013/3/30 Christopher Mayne <mayne_at_ks.uiuc.edu>
>
>> Based on the permissions error, I would suggest opening the tkcon, cd to
>> a local directory in which you have read/write privileges, and rerun the
>> optimization.
>>
>> Christopher Mayne
>>
>>
>> On Mar 30, 2013, at 9:00 PM, Win Liu wrote:
>>
>> Hello vmd developers,
>> I am using fftk plugin to develop a forcefield file for a small organic
>> molecule, but in Opt.charges step, one error occur:
>>
>> #
>> error deleting "base-wat.pdb": permission denied
>> error deleting "base-wat.pdb": permission denied
>> while executing
>> "file delete base-wat.pdb"
>> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 125)
>> invoked from within
>> "::ForceFieldToolKit::ChargeOpt::optimize"
>> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
>> invoked from within
>> "::ForceFieldToolKit::gui::coptRunOpt "
>> invoked from within
>> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
>> invoked from within
>> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
>> .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
>> .fftk_gui.hlf.nb.chargeopt.runOpt in..."
>> (command bound to event)
>> #
>>
>> And I found that this issue is exactly the same as *Esra Bozkurt pointed
>> before, JC pointed out that it's because of the default directory and
>> environment variable in VMD, I think so too, then I move VMD, NAMD and
>> every file else to different directory, but this issue occured still. So
>> can anyone suggest me how to fix this permission issue? By the way, I used
>> windows NAMD. *
>> *
>> *
>> *Thanks in advance! *
>> *
>> *
>> *Wenhao *
>>
>>
>>
>
>