AMBER: PTRAJ problem

From: Beale, John <>
Date: Mon, 26 Feb 2007 12:26:21 -0600

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


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 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?




John Beale



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Received on Wed Feb 28 2007 - 06:07:25 PST
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