[AMBER] ptraj can not read NC file. and not succeed in apply patch.

From: hai wei <weihy61.gmail.com>
Date: Fri, 22 Jul 2011 16:22:46 +0800

Dear Amber community:

I came across the error that ptraj can not read NC file. Then I searched the
topic in Amber mail list, The problem is that I should apply patch to
ambertools. While It seems that I dont know how to apply patch to
ambertools, Here is what I have done:

export AMBERHOME=/home/amber10/amber10 (this is whare i install ambertools)
./apply_bugfix_all.x bugfix.all (both of the file download from

While I kept got the message asking me which file to patch.
pplying all bugfixes in bugfix.all
Patching AMBER installation in /home/amber10/amber10/
Directory exists warnings can be safely ignored.
mkdir: can not make “test/chamber”: already existed
mkdir: can not make “test/chamber/md_engine/”: already existe
mkdir: can not make“dhfr”: already existe
mkdir: can not make “dhfr_cmap”: already existe
mkdir: can not make “dhfr_cmap_pbc”: already existe
can't find file to patch at input line 59
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
|********>Master Bugfix File - AmberTools bugfixes for version 1.5, fixes
|Programs: AmberTools
|Description: This is the master bugfix file for AmberTools-1.5. It
| contains all of the bugfixes released against version 1.5
| in a single patch script.
|Usage: Save this file in your $AMBERHOME directory and then
| apply this patch file to your distribution as follows:
|patch -p0 -N <bugfix.all
|If you have already patched some files the patch program should realise
|and skip them. If you have trouble then you may need to apply each of the
|bug fixes separately.
|********> bugfix 1
|Author: Daniel R. Roe
|Date: 25 April 2011
|Programs: cpptraj
|Description: Enhancements and fixes for cpptraj.
| From version 1.0.5 to 1.0.8.
| - Added "average" keyword to "reference" command. Allows one to average
| the coordinates of an input trajectory and use as a reference struct.
| - Added "precision" keyword to "datafile" command. Users can specify
| an output width and precision for data sets in a data file.
| - Added "maxmin" keyword to "outtraj" command. Users can direct outtraj
| to only print frames that are between a specified max and min based
| on specified data set.
|Bug fixes:
| - Box type detection is now fixed for general triclinic cells.
| - Fixed segfault when reading trajectory with box coords when associated
| parm has no box informaton.
| - Fix potential write of binary characters to Amber trajectory files when
| using "outtraj".
| - General improvement in output and debugging messages.
|From 2521863419ead1a5fb72d37646934ee1f61b7d84 Mon Sep 17 00:00:00 2001
|From: Daniel R. Roe <daniel.r.roe.gmail.com>
|Date: Tue, 22 Mar 2011 16:56:07 -0400
|Subject: [PATCH 014/279] DRR - Cpptraj: Create new Add function for
| AmberTools/src/cpptraj/src/FrameList.cpp | 15 ++++++++++++++-
| AmberTools/src/cpptraj/src/FrameList.h | 1 +
| 2 files changed, 15 insertions(+), 1 deletions(-)
|diff --git AmberTools/src/cpptraj/src/FrameList.cpp
|index 08a5628..7972832 100644
|--- AmberTools/src/cpptraj/src/FrameList.cpp
|+++ AmberTools/src/cpptraj/src/FrameList.cpp
File to patch:

I am not sure which file to patch here.


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Received on Fri Jul 22 2011 - 01:30:02 PDT
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