AMBER Archive (2007)

Subject: AMBER: PTRAJ problem

From: Beale, John (jbeale_at_stlcop.edu)
Date: Mon Feb 26 2007 - 12:26:21 CST

I am trying to generate an AMBER restrt file of an average structure
from between sets 50 and 200 of an MD run. My avg.in file looks like
this:

 

trajin myfile.mdcrd 50 200

center *

image center familiar

rms first mass out avgb_rms.dat *

average myfile.rst restrt

 

When I run ptraj using this avg.in file, the program runs up to the
point where it dumps data. Then the following happens:

 

PTRAJ: Successfully read in 200 sets and processed 151 sets

            Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs. time data

Segmentation fault (core dumped)

 

Does anyone have any suggestions as to what I might be doing wrong and
how I can correct the problem of generating a restrt file out of ptraj?

 

Thanks,

 

John Beale

 

 

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