From: Hyunjin Kim (hyunjink_at_andrew.cmu.edu)
Date: Mon May 04 2015 - 13:49:06 CDT

Thanks. It is fixed. It was not problem with the bonded optimization tool
but with the path for the namd executable. Thanks.

> Hyunjin,
>
> The error message is not particularly informative, so I have a couple of
> requests to try and track this down.
>
> 1) Did the attempted optimization generate any LOG files (e.g.
> BondedOpt.log)? If so, please send them to me.
>
> 2) Can you rerun with "Write debugging log" (under Advanced Settings)
> turned on and send me any LOG files that are generated (e.g.,
> BondedOpt.log and BondedOpt.debug.log)
>
> 3) Outside of VMD, can you run NAMD from the folder containing the
> configuration and temp parameter files (i.e., min-bondangles.conf,
> OPTTEMP.par, etc)? Something like
> path/to/namd2.exe min-bindangles.conf > test.log
>
> Thanks,
> Christopher Mayne
>
> On May 4, 2015, at 11:37 AM, Hyunjin Kim wrote:
>
>> Thanks. I attach the error text as a file.
>>
>>
>>> Hyunjin,
>>>
>>> Please cc VMD-L on your email so that others can benefit from the
>>> discussion.
>>>
>>> The use of relative paths for OPTTEMP and min-bondangles should be OK
>>> since clicking the "Run Optimization" both creates the temp files, and
>>> then runs NAMD from the CWD in the background; these files are deleted
>>> prior to returning control to the GUI. Rather than assuming this is
>>> the
>>> error, can you tell me what the exact error text is?
>>>
>>> Regards,
>>> Christopher Mayne
>>>
>>>
>>> On May 4, 2015, at 11:21 AM, Hyunjin Kim wrote:
>>>
>>>> Thanks. That fixed the error.
>>>> When I click the "Run Optimization", fftK automatically generates
>>>> "min-bondangles.conf" file and the OPTTEMP.par" is generated in the
>>>> same
>>>> directory as the other files located. However, the following lines in
>>>> the
>>>> "min-bondangles.conf" do not include proper paths unlike the other
>>>> lines
>>>>
>>>> parameters OPTTEMP.par
>>>> outputName min-bondangles
>>>>
>>>> Please see the attached file. This gives me another error. What do I
>>>> have
>>>> to do to set the path for these lines?
>>>>
>>>> Thanks.
>>>>
>>>> Hyunjin.
>>>>
>>>>
>>>>
>>>>> Hyunjin,
>>>>>
>>>>> This is most likely because the upon startup the CWD for Windows
>>>>> installs
>>>>> in the protected portion of the disk. Try opening the Tk Console
>>>>> (Extensions -> Tk Console) and 'cd' to a directory where you have
>>>>> write
>>>>> privileges, e.g., your home directory.
>>>>>
>>>>>
>>>>> Chris
>>>>>
>>>>> On May 3, 2015, at 2:55 AM, Hyunjin Kim wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> When I ran "simulated annealing" for optimizing bonded parameters,
>>>>>> the
>>>>>> following error occurred:
>>>>>>
>>>>>> "Cannot write to CWD (required for temporary files)".
>>>>>>
>>>>>> This error seems to occur, since I do not define "output path" for
>>>>>> the
>>>>>> working directory before this optimization. However, I do not have
>>>>>> idea
>>>>>> how to do.
>>>>>>
>>>>>> I am using "vmd192beta1win32".
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Hyunjin.
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> <min-bondangles.conf>
>>>
>>>
>> <ba.log>
>
>