From: John Stone (
Date: Thu Feb 08 2018 - 16:24:26 CST

  It is up to you what IMD port is used for interconnection between
NAMD and VMD. You can set this in the NAMD config file, and also in
the VMD graphical interfaces (and/or text commands). I'm not familiar
with the particular steps you're trying to follow, but if you read
the documentation for the IMD features of VMD and NAMD you can set
the port for the IMD connection, which addresses the specific question
you had below.

  John Stone

On Thu, Feb 01, 2018 at 09:17:27AM +0000, De Winter Hans wrote:
> Dear all,
> I am a newby in the use of VMD, so maybe my question was already posted
> and replied in this list (although I could not find a similar one in the
> archives). Currently I am reproducing the tutorial on 'Structure Check',
> in which the wrong chirality of some nucleic acids is corrected and the
> structure optimized using the 'Fix Chirality Errors' extension. This
> extension generates a temporary NAMD input file and then connects to NAMD
> using AutoIMD.
> The problem I have is that the execution is not reproducable, in which I
> mean that initially it all works fine, but after a couple of chirality
> fixes there seems to be a problem in connecting VMD with NAMD. The port on
> which these connect seems to vary, for example during the same session I
> got these two attempts:
> ERROR) Error connecting to localhost on port 2294
> and
> ERROR) Error connecting to localhost on port 5591
> Any clues? I am running VMD on Mac OS X, version 10.13.3 (High Sierra). I
> also tested it in our Ubuntu systems, but here we found no issues at all.
> So it seems to be OS X related.
> Many thanks in advance,
> Hans

NIH Center for Macromolecular Modeling and Bioinformatics
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