VMD-L Mailing List

From: João Ribeiro KS (jribeiro_at_ks.uiuc.edu)
Date: Tue Feb 28 2017 - 07:56:40 CST

Dear Danu,

the error that you described was originated from the fact that namd could
not find the configuration file (CKMD.namd).
The platform that I ask about was your operating system (Mac, Windows or
Linux), not the VMD version (for future reference).

You can always try to prepare your structure and run the simulation with
QwikMD, which by the way, also uses autopsf to prepare the structure.

Best

Joao

On Sun, Feb 26, 2017 at 10:50 AM Danu Fajar <dfr879_at_gmail.com> wrote:

> Hi Joao
>
> I can confince you that the path is correct and I can see the file inside
> that path.
> I use version 1.9.3 platform
>
> Is the PSF file that I created from auto PSF could be the problem?
> the Input files was the PDB that I downloaded from rscb.org
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__rscb.org&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=TZnc8ccCfWWjgkZxL3lh5blIMo0Ud-MHt62nw-ZKJE0&m=gE64kC3bRdlWEblhQBW78eO5SaGbqlTjLBO9dEKI3cI&s=crs9KYxdaZD-lNWOk-Up2xuO1aZTkidlWL2uRdWx9Fw&e=>
> and for the input of PSF file, I use "automatic PSF builder" to make the
> PSF file from the PDB that I downloaded.
>
> Or Should I use QwikMD for easier way including prepare the PDB and PSF ?
> or will it be more complicated ?
> Actually I haven't try the QjwikMD.
>
> Best Regards,
> Danu
>
> On Fri, Feb 24, 2017 at 12:52 AM, João Ribeiro KS <jribeiro_at_ks.uiuc.edu>
> wrote:
>
> Hi Danu,
>
> sorry for the delay. Before the line starting as "FATAL ERROR:..." there
> is a line starting with "info:" stating the FULL PATH of the configuration
> file. Is that path correct? Can you find the file inside that path?
>
> Another question that I should have done in the beginning, on which
> platform are you running VMD and NAMD?
>
> Best wishes
>
> Joao
>
> On Sat, Feb 11, 2017 at 12:03 PM Danu Fajar <dfr879_at_gmail.com> wrote:
>
> Hi Joao,
>
> Thank you for the link of tutorials, I'm sorry to made you do that because
> I didn't read whole tutorials, and unfortunately I miss those tutorials. I
> think I need to study from the begining of NAMD tutorials. but if you find
> anymore solution for my problems, please tell me.
>
> Here comes another problem, in CKMD.out file, it said
> "FATAL ERROR: Unable to access config file CKMD.namd"
>
> And when I tried to open th CKMD.namd file which is created in the same
> folder as CKMD.out file, it's just shows the parameters of simulation. I
> think don't find any error in this file.
>
> So what's wrong with it ?
>
> It's okay if you can't help me anymore. I just don't want you to feel
> burdenned with these problems..
>
> Best Regards,
>
> Danu
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3000380 <(217)%20300-0380>
>
>
> --
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380