Thank you to everyone for your replies. I am sure that I am using the right prmtop file, and it is a periodic simulation, so that part should be okay as well. (I also checked the size of the files, as suggested, and found that the concatenated file was significantly less than the summed size of the two smaller files, so my first attempt at concatenation definitely did not work properly.)
As a long shot I tried submitting the job to the AMBER 7 version of ptraj (my previous attempts had used AMBER 8). It worked fine on AMBER 7, producing a mdcrd file of the right length. I was able to use this new mdcrd file as the "trajin" file for another job without any problems.
Has anyone else experienced such differences between AMBER 7 and AMBER 8? Is there some difference in ptraj inputs between AMBER 7 and 8 that I am not aware of?
Thank you very much for all of your input.
Adam
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Received on Sun Jun 04 2006 - 06:07:21 PDT
