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On 2. Jun 2023, at 16:26, Bhattacharjee, Sinjini <bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>> wrote:
Hi, I am trying to minimise a protein-membrane system using sander and pmemd in Amber20. However, the calculation keep crashing in the first cycle with the following error:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.0669E+24 C19 90066
BOND = 31692.7352 ANGLE = 68711.0955 DIHED = 59597.8979
VDWAALS = NaN EEL = -12389.2862 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = -149672.0786 RESTRAINT = 0.0000
This is my initial input:
Minimize
System minimization:
&cntrl
imin=1, ntmin=1, nmropt=0
maxcyc=2000, ncyc=1000,
ntx=1, irest=0,
ntpr=100, ntwr=100, iwrap=0,
ntf=1, ntb=1, cut=10.0, nsnb=20,
igb=0,
ibelly=0, ntr=1,
restraintmask=?.CA", restraint_wt=20.0,
&end
/
I added the membrane using packmol-memgen.
The system size is huge and I checked and removed clashes in the protein and the non-standard residues.
Can you please tell me what is the problem and how can I solve this? Is it an issue with the parameters or the structure?
Many thanks,
?
Sinjini Bhattacharjee
PhD Student
Molecular Theory and Spectroscopy
Max-Planck-Institut f?r Kohlenforschung
45470 M?lheim an der Ruhr, Germany
email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
---
------------------------------
Message: 4
Date: Wed, 7 Jun 2023 13:12:40 -0400
From: Evan Biedermann <ebiedermann.cloud303.io>
To: amber.ambermd.org
Subject: [AMBER] Trouble Installing OpenMPI on Amazon Linux 2 (CentOS)
Message-ID:
<CALu0Rodscp94Db0UYgO4ELw5_pJTMVpj6O7c8CxemBnuoqhmeA.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hello,
*Problem Summary:*
I am having an issue installing Amber22 with CUDA and MPI. I have followed
the directions for installing in centos using cmake following both
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_InstCentOS.php&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=fkpyze4KaEV4v9mRgnd-3PzECwR27SqX8UjgLKdHuwo&e= and https://urldefense.proofpoint.com/v2/url?u=https-3A__ambermd.org_doc12_Amber22.pdf&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=GSDHuwZmM965TqNr8Kd3Eok1AZy1EhJ_SP7IjIgmjzs&e= .
I ran the initial install following the step 3 of page 23 on the pdf
instructions. Then I installed the MPI compilers in the
$AMBERHOME/AmberTools/src path as specified in step 8 of page 24. After
that, I went back to the run_cmake file, set DMPI=TRUE, and ran sudo
./run_cmake.
The mpifort and mpif90 compilers are in the same path as the MPI C and MPI
CXX Compilers, but for some reason cmake is unable to find them. I have
tried adding the path to .bashrc, adding set(MPI_Fortran_COMPILER
/opt/amber22/AmberTools/src/bin), set(MPI_Fortran_INCLUDE_PATH
/opt/amber22/AmberTools/src/bin), set(MPI_Fortran_LIBRARIES
/opt/amber22/AmberTools/src/bin) to the MPIConfig.cmake and CMakeList.txt
files and nothing has worked. I have also tried setting the INCLUDE_PATH
and LIBRARIES to /opt/amber22/AmberTools/src/lib/openmpi.
To add more specifics, I originally installed the version of OpenMPI by
using wget to download openmpi-4.1.5.tar.bz2 to $AMBERHOME/AmberTools/src,
unpacking and installing following these commands:
1. *tar -xzf openmpi-4.0.1.tar.gz*
2. *cd openmpi-4.1.5*
3.
*./configure --prefix=/opt/amber22/AmberTools/src *
4. *make*
5. *sudo make all install*
This ended up with the following bin folder in this
path: /opt/amber22/AmberTools/src/bin
[image: image.png]
(if the picture does load, the bin contains mpicc, mpicxx, mpif77, mpirun,
mpiCC, mpiexec, mpifort, mpif90, mpic++....)
Here are the full details on the system I'm using:
*NAME="Amazon Linux"VERSION="2"ID="amzn"ID_LIKE="centos rhel
fedora"VERSION_ID="2"PRETTY_NAME="Amazon Linux
2"ANSI_COLOR="0;33"CPE_NAME="cpe:2.3:o:amazon:amazon_linux:2"HOME_URL="https://amazonlinux.com/
<https://urldefense.proofpoint.com/v2/url?u=https-3A__amazonlinux.com_&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=DqKss6ZME-Nclx648etewDYojsHCFtJEbqMk7vv63uo&e= >"*
*Description: Amazon Linux release 2 (Karoo)*
I do believe that the issue is coming from a base version of mpi
interfering with the one I tried to install, because originally when I used
the command *which mpif90* it would show a path to */efs/anaconda3/bin*. I
then tried *sudo yum install openmpi-devel* and *module load mpi* and
now *which
mpif90* gives */opt/amazon/openmpi/bin/mpif90* and *mpif90 --version*
gives:
*GNU Fortran (GCC) 7.3.1 20180712 (Red Hat 7.3.1-15)*
*Copyright (C) 2017 Free Software Foundation, Inc.This is free software;
see the source for copying conditions. There is NOwarranty; not even for
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.*
However, the Amber build is still failing giving the same output as the
original error:
*--
**************************************************************************--
Starting configuration of Amber version 22.0.0...-- CMake Version: 3.26.4--
For how to use this build system, please read this wiki:--
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_pmwiki_pmwiki.php_Main_CMake&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=t2AFYkRZJ8liHA48DtSJeNVCjiM2CFbRxaqLl8YQMz4&e=
<https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_pmwiki_pmwiki.php_Main_CMake&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=t2AFYkRZJ8liHA48DtSJeNVCjiM2CFbRxaqLl8YQMz4&e= >-- For a list of important
CMake variables, check here:--
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_pmwiki_pmwiki.php_Main_CMake-2DCommon-2DOptions&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=_uB3HG8j4Lx420daHZhVHQY2vDr0QRi5AJe7pvYxVZY&e=
<https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_pmwiki_pmwiki.php_Main_CMake-2DCommon-2DOptions&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=_uB3HG8j4Lx420daHZhVHQY2vDr0QRi5AJe7pvYxVZY&e= >--
**************************************************************************--
Amber source found, building AmberTools and Amber-- Could NOT find
MPI_Fortran (missing: MPI_Fortran_WORKS)-- Could NOT find MPI (missing:
MPI_Fortran_FOUND) (found version "4.0")-- MPI C Compiler:
/opt/amber22/AmberTools/src/bin/-- MPI CXX Compiler:
/opt/amber22/AmberTools/src/bin/CMake Error at cmake/MPIConfig.cmake:16
(message): You requested MPI, but the MPI Fortran library was not found.
Please install one and try again, or set MPI_Fortran_INCLUDE_PATH and
MPI_Fortran_LIBRARIES to point to your MPI.Call Stack (most recent call
first): CMakeLists.txt:120 (include)-- Configuring incomplete, errors
occurred!If errors are reported, search for 'CMake Error' in the cmake.log
file.If the cmake build report looks OK, you should now do the following:
make install source /opt/amber22/amber.shConsider adding the last line
to your login startup script, e.g. ~/.bashrc*
It looks like the MPI C and MPI CC compilers are still being sourced from
/opt/amber22/AmberTools/src/bin/ but it can't find the fortran compiler.
I've tried removing /opt/amber22/AmberTools/src/bin/ from the PATH to use
the yum install, but the build is still
sourcing /opt/amber22/AmberTools/src/bin/ for MPI C and MPI CC.
Please let me know how I can resolve this issue.
Best,
Evan
--
Evan Biedermann
Associate Solutions Architect
Engineering | Cloud303
ebiedermann.cloud303.io
cloud303.io
12081 W Alameda Pkwy, Suite 150, Lakewood, CO 80228
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.hubspot.com_email-2Dsignature-2Dgenerator-3Futm-5Fsource-3Dcreate-2Dsignature&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=VVFhkwOayiCM_6CEInd5GGUM-4GIcNbucJale2YmvBs&e= >
------------------------------
Message: 5
Date: Wed, 7 Jun 2023 14:46:53 -0400
From: Prithviraj Nandigrami <prithviraj.nandigrami.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] H-bond analysis in cpptraj
Message-ID:
<CABh86xPq_-9PB4m-UzDObx0iZmfvV0cx8FTk__oc=CMCSgODnw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear AMBER Users and Experts,
Could someone please guide me on how to print out the total number of
hydrogen bonds formed between solute-solute (excluding the solvent) in a MD
trajectory?
I am using the following script:
parm input.parm7
trajin input_no_WAT.nc
hbond Backbone :1-90.C,O,N,H avgout BB.avg.dat series uuseries bbhbond.gnu
How do I calculate the total number of H-bonds formed in each frame
during the course of an MD run?
Many thanks for your help in advance.
PN
------------------------------
Message: 6
Date: Wed, 7 Jun 2023 14:56:41 -0400
From: Prithviraj Nandigrami <prithviraj.nandigrami.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Native contacts analysis in CPPTRAJ
Message-ID:
<CABh86xMTR814LxOoE3-chbeTGoFq_23eYgd0Wtz8G91TWnvdbQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear AMBER Users and Experts,
I am trying to use the native contacts analysis script implemented in
CPPTRAJ for a couple of MD trajectories as follows:
parm input.strip.parm7
trajin combined.strip.nc <https://urldefense.proofpoint.com/v2/url?u=http-3A__combined.nc_&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=Xd20vFCFTCcm8jERS0EyWnag9kuJYMBLpwow-1jNXFWy4fqMvRqRxCq_MRuD8fhf&s=72qL5Repo2zkyWJbaHeFvE0I2gOjd5O-tlemlGOIDhc&e= >
nativecontacts name NC1 :1-85&!.H= \
writecontacts native-contacts.dat \
resout resout.dat \
distance 5.0 \
byresidue out all-residues.dat mindist maxdist \
map mapout gnu \
contactpdb contactspdb.pdb \
series seriesout native-contacts-series.dat
run
lifetime NC1[NC] out lifetime.dat
run
Here is an example for native.gnu file:
1.000 1.000 0.0000
1.000 2.000 16.6333
1.000 3.000 0.0000
1.000 4.000 0.0000
1.000 5.000 0.0000
1.000 6.000 0.0000
1.000 7.000 0.0000
1.000 8.000 0.0000
1.000 9.000 0.0000
1.000 10.000 0.0000
I have two sets of MD runs - wild-type protein and mutant protein. I used
the script above to calculate native.gnu files for these two systems.
I was looking to plot a "difference" plot for these two systems with the
hope that regions with the most significant differences would show up.
What is the correct way to go about this? If I take the difference of the
third column (normalized) for the wild-type and mutant cases, and try to
plot a contact map, is that it?
I would appreciate any help or guidance.
Thank you.
P.N.
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Received on Thu Jun 08 2023 - 12:00:02 PDT