VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Dec 10 2012 - 17:50:06 CST

This is not an fftk-specific problem. Rather, you must not have write permissions to your temp directory - I guess it's a Windows related issue? Hopefully someone else on the list can comment, or suggest how to change the default directory. I'm sure it's stored in an environment variable of some sort in VMD.

On Dec 10, 2012, at 1:21 PM, Esra Bozkurt wrote:

>
> Hello,
>
> I am writing in response to an error message that I have during parametrization of a new ligand. I was wondering if you can help me to solve the problem.
>
> What I would like to do is to parametrize a new ligand for Charmm Force Field and then use it for my MD simulation. With this aim, I am using VMD 1.9.1, I have also downloaded namd, and I download the videos (8 videos) in the web-site for ligand parametrization. I am in the step 5 (5-charges-2-optimization). In the Opt. Charges part of Force Field Toolkit , when I run the optimizaton after uploading necessary files, I have this error message :
>
> 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)
>
> I guess that it arises from the water-sp.log file in the example video, since I didn't understand what is exactly this file contains? I uploaded a single water molecule that I generated with random coordinates and I runned a single point energy calculation with # RHF/6-31G* Opt=(Z-matrix,MaxCycles=100). Also, after pressing run optimization , when I check the TK Console I observed that it finds a stationary point, but "no mulliken charges were found message" also appears!
>
> Could you please help me to solve the problem?
>
> Thanks in advance for your consideration,
> Kind regards,
> Esra Bozkurt
>
>