Hi,
What version of AmberTools do you have? Although you say you
downloaded from
http://ambermd.org/bugfixes10.html, the bugfix.all
you attempted to apply appears to be for AmberTools 1.5:
> |********>Master Bugfix File - AmberTools bugfixes for version 1.5, fixes
Bug fixes from AmberTools 1.5 are not compatible with amber10. If you
are not using AmberTools 1.5 I recommend that you upgrade - be aware
that it does install in a separate directory (amber11) from Amber 10.
If you need to apply amber10 bug fixes make sure you are using this bugfix.all:
http://ambermd.org/bugfixes/10.0/bugfix.all
-Dan
On Fri, Jul 22, 2011 at 4:22 AM, hai wei <weihy61.gmail.com> wrote:
> 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
> http://ambermd.org/bugfixes10.html).
>
> 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
> 1-10
> |
> |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:
> |
> |cd $AMBERHOME
> |patch -p0 -N <bugfix.all
> |
> |If you have already patched some files the patch program should realise
> this
> |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.
> |Enhancements:
> | - 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
> framelist
> |
> |---
> | 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
> 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.
>
> Thanks
>
> haiya
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 22 2011 - 04:30:03 PDT
