VMD-L Mailing List

From: Danu Fajar (dfr879_at_gmail.com)
Date: Fri Feb 10 2017 - 13:31:38 CST

Thank you for back response Joao,

Can you explain those different purposes for those plugins ?
I don't really know about that since I'm a newbie in MD

And how can I open th CKMD.out file?
When I tried to open it, it needs to know what program I should use.

Best regards,

Danu

On Fri, Feb 10, 2017 at 10:52 PM, João Ribeiro KS <jribeiro_at_ks.uiuc.edu>
wrote:

>
> Hi Danu,
>
> please reply to "all" so we can keep track of the answers to this question
> in the mailing list.
>
> From what you described, you must be using NAMDGui instead of QwikMD.
> These are different plugins with different purposes.
>
> Please open the CKMD.out file, which is the namd log/output file, and
> check for errors in the end.
>
> Best
>
> Joao
>
> On Fri, Feb 10, 2017 at 9:30 AM Danu Fajar <dfr879_at_gmail.com> wrote:
>
>> Hi Joao, thank you for response and try to helping me.
>> I think I do use QwikMD plugin, beacuse I found it in the folder.
>>
>> .) these are the steps:
>> 1. I was download the NAMD version 2.12 (and also try for 212b) for win
>> 64 from http://www.ks.uiuc.edu/Development/Download/download.
>> cgi?PackageName=NAMD
>>
>> 2. the whole extracted file (including "namd2.exe) was extracted in the
>> same folder with VMD application
>> (C:\Program Files (x86)\University of Illinois\VMD)
>>
>> 3. Open VMD, and run the NAMD simulation from GUI
>>
>> 4. soon after I run NAMD, the tools which said "namd2.exe stopped
>> working" appeared
>>
>>
>> .) Here is the last message in TK Console:
>>
>> 5514 atoms total
>> Starting NAMD...
>>
>> .) and the last message in CMD
>>
>> info> Finished with coordinate file CKMD_fixed.pdb
>> info> Finished with coordinate file CaseinKinase_formatted_
>> autopsf_formated.pdb
>>
>> .) the log file created was CKMD.namd (NAMD file) and CKMD.out (OUT file)
>>
>> that's all information I have for now, so I really don't know what to do--001a1140bf58838304054832254c--