AMBER: Nmode segmentation fault

From: James Thomas <>
Date: Tue, 25 Mar 2008 11:53:21 +0000

Dear amber community

I am running a nmode program using amber9 package. I tried using a smaller
file as a test (the prmtop size: 566999 & the inpcrd: 50451). My interest
protein has this (the prmtop size: 2307687 & the inpcrd size:210978).
However, I got the error message of segmentation fault few minutes after I
started the run.

My test run using test protein is successful to complete 100 steps of Newton

I also refer this :, but not
sure on how to modify the alloc.f file.

Is that because my protein of interest is too big?

I look forward to your advices / suggestions.

Many thanks!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:13:54 PDT
Custom Search