I was using NAMD for simulating my protein-ligand complex via its interface VMD and all was fine until i clicked run NAMD. it stopped running everytime i ran it.. And the application error box says error deleting dock_md.out permission denied (please find out the attachment for the snapshot of the application error) I'm working on 64 bit version of NAMD but 32bit version of VMD on windows.
This error is not because of 64 bit.
This error may be caused by NTFS permissions since you are running from Windows.
Try to change permission by browse c:\program files\NAMD folder then right-click on the file or folder, choose Properties and then go to the Security tab.
If you have no access to the folder, you’ll see a message stating you have to be an Administrator to view the security properties. Go ahead and click on Continue. This will pop up another dialog where you get the option to change the owner.
In the Change owner to box, select your user account or Administrators.
UBUNTU is best platform for NAMD.
Hope this will help you.
Best!!
Basically, running NAMD under Windows is not the most optimal way. I've never tried to launch it using VMD as it doesn't have much sense, but you may try at least a couple of solutions:
1. simply ommit vmd an run NAMD directly with vmd-generated inputs
2. Change your working directory. Win may be suspicious when you work directly in C
3. Ommit white spaces in your filename
4. run VMD in an administrator mode
good luck.
Although I also agree that it should be much better running NAMD under Linux than under Windows, the program is usually run without problems in command mode in a DOS window just as it would be done in Linux.
I suggest preparing the input files with VMD and then run NAMD in command mode. In any event, as Dr. Jakubowski says, it should be a good idea run VMD in administrator mode (right clik on the VMD icon and select this option) and work on a separate folder created for your calculations.
In principle, working with 32 bit-VMD and 64 bit-NAMD should not cause your problems
This error is not because of 64 bit.
This error may be caused by NTFS permissions since you are running from Windows.
Try to change permission by browse c:\program files\NAMD folder then right-click on the file or folder, choose Properties and then go to the Security tab.
If you have no access to the folder, you’ll see a message stating you have to be an Administrator to view the security properties. Go ahead and click on Continue. This will pop up another dialog where you get the option to change the owner.
In the Change owner to box, select your user account or Administrators.
UBUNTU is best platform for NAMD.
Hope this will help you.
Best!!
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