Hello,
Sorry for the long delay on this. I started working on this problem
with some people off-list and forgot to reply to the mailing list when
it was sorted out.
It turns out the cmake build of Amber does not properly link the
readline library for cpptraj; cpptraj uses readline for its
interactive mode. This should be fixed in the next release of
AmberTools.
If you want a fully functional cpptraj (with interactive support) with
AmberTools 20 you will need to build it separately, either inside the
Amber source tree or using the GitHub version
(
https://github.com/Amber-MD/cpptraj). So for example, to build
cpptraj inside the Amber source tree:
# Ensure Amber environment is set up
source $AMBERHOME/amber.sh
# Change to the cpptraj directory
cd $AMBERHOME/AmberTools/src/cpptraj
# Configure cpptraj; replace 'gnu' with whichever compilers you used
to build Amber
./configure --prefix=$AMBERHOME -amberlib gnu
# Build and install
make -j2 install
This should result in a functioning cpptraj being installed to your
$AMBERHOME/bin directory. If you want OpenMP or MPI, specify the
'-openmp' or '-mpi' flags to cpptraj's configure script. Hope this
helps,
-Dan
On Thu, Feb 25, 2021 at 1:12 PM Cato, Lee <michael.lee.cato.emory.edu> wrote:
>
> I am having an issue with Amber20 installation. I have applied all patches, all tests have passed, and simulations as well as programs such as antechamber work fine. However, when I try to use cpptraj, I get this output:
>
> CPPTRAJ: Trajectory Analysis. V4.25.6
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 02/25/21 13:00:05
> | Available memory: 977.785 MB
>
> Loading previous history from log 'cpptraj.log'
> Segmentation fault (core dumped)
>
> I have tried everything from reinstalling without update2 (cpptraj patch), reinstalling with all patches, and I have tried to debug the file with no avail.
>
> Note that if I move the executable cpptraj file from a previous build (amber16), I am able to run cpptraj fine.
>
> Can you please help with this????
>
> Best,
> Cato
>
> --
> Ph.D. Candidate
> Biochemistry, Cell, and Developmental Biology Program
> Ortlund Lab
> Emory University
>
> ________________________________
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 13 2021 - 06:30:02 PDT
