From: Soumya Lipsa Rath (soumyalipsabt_at_gmail.com)
Date: Mon Feb 01 2016 - 20:07:49 CST

Dear Dr. Mayne,

Thanks! that worked. But again what do I do about the other log files. Say
if I scan the dihedral for 90 degrees (18 steps with 5 degrees each), in
the first time it runs 10 steps and terminates due to wall time error, then
I restart from the checkpoint file and get another log file. Should I
ignore the rest of the log files?

Thanks,
Soumya

On Tue, Feb 2, 2016 at 10:58 AM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Soumya,
>
> Without seeing the log files, I would assume that #1 is the problem. The
> ffTK parser reads some information from the beginning of the LOG files to
> define the dihedral that is being scanned. My guess is that this data
> isn’t replicated in the LOG files that result from a restart. Try loading
> in the first LOG file.
>
> Regards,
> Christopher
>
> On Feb 1, 2016, at 6:19 PM, Soumya Lipsa Rath <soumyalipsabt_at_gmail.com>
> wrote:
>
> Dear Dr. Mayne,
>
> Thanks for your reply.
>
> 1) I am passing on the log files from gaussian. Although, during the
> calculation, I had to restart gaussian 2-3 times, and I am loading the last
> log file. Is that the problem? If so, could you please tell me how to
> rectify the same.
>
> 2) I am using vmd version 1.9.2
>
> 3) Yes, the gaussian terminated normally. They also ran few steps before
> terminating.
>
> Thanks,
> Soumya
>
> On Tue, Feb 2, 2016 at 3:34 AM, Mayne, Christopher G <cmayne2_at_illinois.edu
> > wrote:
>
>> Soumya,
>>
>> Something is amiss with the parser. There’s not much information go on
>> here, so I have a few questions:
>>
>> 1) Make sure that you’re passing it the LOG files output from the
>> Gaussian calcaulation.
>>
>> 2) What version of VMD are you using?
>>
>> 3) Did you check the Gaussian LOG files to ensure that they ran? (they
>> don’t necessarily need to complete without error, but they need to make it
>> a few steps)
>>
>> Regards,
>> Christopher Mayne
>>
>>
>>
>> On Feb 1, 2016, at 12:27 AM, Soumya Lipsa Rath <soumyalipsabt_at_gmail.com>
>> wrote:
>>
>> Hi,
>>
>> I am using the FFTK toolkit of vmd for developing CHARMM compatible
>> parameters. During the "Dihedrals I: Generating Dihedral Scan Target Data"
>> step, when I am trying to load the log files, I am getting the following
>> error.
>>
>> can't read "scanDihDef": no such variable. I am using Gaussian 09 for
>> running the scans. Please help me figure out the problem.
>>
>> Thanks,
>> Soumya
>>
>>
>>
>>
>>
>>
>>
>
>