AMBER Archive (2003)

Subject: AMBER: Nmode problem

From: Wu Yingliang (wuyliang_at_public.wh.hb.cn)
Date: Fri Nov 28 2003 - 07:52:31 CST

Dear Amber users,

I am using amber7 in Red Hat Linux 9.0. There are something wrong with Nmode. When I test Nmode in $AMBERHOME/test directory, some possible failures appear. At first, I did not care about it. However, examples of "Nmode" calculation for estimating entropies by MM-PBSA can not be correctly run. In addition, I can not find AMBER 7.0 Bug Fixes from Amber web. Some relative informations are as following:

[whu_at_localhost test]$ make test.nmode
cd nmode; ./Run.ala-dipeptide
  
NMODE: find normal modes
diffing vibs.out.save with vibs.out
PASSED
==============================================================
  
NMODE: find Langevin modes
diffing lvibs.out.save with lvibs.out
PASSED
==============================================================
diffing lmode.head.save with lmode.head
PASSED
==============================================================
  
cd newton_raph; ./Run.newton_raph
diffing nmd_min.out.save with nmd_min.out
possible FAILURE: check nmd_min.out.dif
==============================================================
cd quasih; ./Run.quasih
 Title in input file:
 rdparm transformed trajectory
  
diffing quasih.out.save with quasih.out
possible FAILURE: check quasih.out.dif
==============================================================
[whu_at_localhost test]$

Looking forward to help! Thanks a lot in advance!

Best Regards,

Wu Yingliang
2003-09-19
==================================
College of Life Sciences
Wuhan University
Wuhan 430072
China
Email: wuyliang_at_public.wh.hb.cn
==================================

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