Thanks. I download the he bugfix.all for AmberTools 1.2 and it works.
Thanks.
2011/7/22 Daniel Roe <daniel.r.roe.gmail.com>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
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Received on Sat Jul 23 2011 - 16:00:02 PDT
