From: De Winter Hans (
Date: Thu Feb 01 2018 - 03:17:27 CST

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


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,