generated ligand-receptor complex from autodock.
Generated a psf file for ligand and receptor seperately and also as a complex.
When I load these files into NAMD and run it, the program crashes.
I am afraid that with that little information it will be impossible to know. What is exactly the error you get?
I do not get any error. The program just crashes. I am able to simulate the receptor alone. But unable to simulate the ligand-receptor complex. However I have a psf file for the complex.However when I run the program in a 32 bit system the error I get is this: can't read namd_fd: no such variable found
If you search your NAMD output for the phrase "FATAL" or print the last few lines of your output here, we may be able to help. Otherwise, there is too little information to work with, unfortunately.
My best guess from what information you have given is that your ligand is not parameterized correctly. You may want to take a closer look at the outputs you have from that process.
If there really isn't any error message, its probably due to memory issue. No. of molecules may be very large and the memory is not sufficient.
Thank you all for the prompt answers. I have got the program running. It was an issue with the environmental path setting. However, there is another problem. I have generated a pdb file of my ligand-receptor complex from Autodock. When I convert it into a psf using auto psf builder, only my receptor (protein) gets converted to a psf. I have parametrized my ligand and generated a psf file seperately. I found this out only after running my simulation. Please help.......
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