Re: FEP on an amino acid ligand

From: JC Gumbart (
Date: Wed Jan 23 2013 - 11:29:57 CST

No idea.

If the mutator plugin breaks, it should be fixed. Send me off-list the files (if they aren't too big) and an exact description of what you tried that crashed it.

On Jan 23, 2013, at 12:21 PM, Thomas Albers wrote:

> Hello!
> On Wed, Jan 23, 2013 at 12:16 PM, JC Gumbart <> wrote:
>> I have no idea what you're trying to do here, but it looks very non-standard. Try using the Mutator plugin in VMD on your original structure (with the FEP box checked) to produce the files you need.
> But it works. :-) The Mutator plugin actually has its own problems,
> when I was using it to mutate the glycine molecule that sits in the
> binding pocket the plugin always crashed.
> Anyway, I downloaded the NAMD-2.9-Linux-x86_64-ibverbs binary, and
> that one works fine on our cluster. The one that we compiled
> ourselves does not. Would you have any hunch what went wrong during
> compilation.
> Regards,
> Thomas

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:54 CST