VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Wed Nov 18 2009 - 11:43:00 CST

Hi Sarah,

In the future, please make sure that you respond on the VMD list instead of just replying to a single person.

It is quite difficult to understand what is going on with your particular problem without more information about the specific errors. If the other molecule is not defined in the topology and parameter files, VMD is not going to know what to do with the corresponding atoms. What is this other molecule that you are trying to simulate?

Josh

On Nov 18, 2009, at 11:09 AM, sarah k wrote:

> Hi again, Josh. Thanks for your previous advisement. The error was fixed and the window claiming that the process is done successfully was popped. The _autopsf.pdb and _autopsf.psf files were created but something awful was happened! The protein is ok but the other molecule is destroyed! Just few atoms are left in the file. My rest of project is based on the very molecule. Why it has happened? How can I fix it?
> feel lucky forever,
> sarah