AMBER Archive (2009)

Subject: [AMBER] decomposition and calculation of entropy

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Sat Oct 10 2009 - 01:13:49 CDT

Hi amber users, I am performing free energy decomposition analysis for a protein-protein interaction case by mm_gbsa (amber10). The calculation goes well for all com, rec and lig, but when it comes for amber to give the statistics.out file the program stops the process and gives the following error, Reading files Reading ll_com.all.out Missing BELE for MM in 1 (residue 358)   And also when calculating the entropy, there are still problems. It showed in the terminal window like this:   /usr/local/amber10/exe/nmode -O -i ........ not running properly   I don't know how this happened?     The attached files are the input and output files for the two problems! (I don't attach the two files, 1sve_com..all.out and 1sve_rec.all.out, in the decomp folder, because they are too big to attach, 25M. And I want to know why the file 1sve_lig.all.out is so small)   Any response will be highly appreciated! Thanks very much!     Qinghua


  • application/octet-stream attachment: Nmode.rar

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