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German P. Barletta pgbarletta

7 followers · 5 following
  • Institute for Quantitative Biomedicine (IQB)
  • Piscataway, New Jersey
  • 07:40 (UTC -04:00)
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@pgbarletta
pgbarletta / gist:e6b68d2e4bd2a842e701ba6659add4af
Created February 21, 2025 21:45
pip install -e . output
Obtaining file:///home/pb777/apocharmm
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: netcdf4 in /home/pb777/miniforge3/envs/apo/lib/python3.11/site-packages (from charmm==0.0.1) (1.6.4)
Requirement already satisfied: cftime in /home/pb777/miniforge3/envs/apo/lib/python3.11/site-packages (from netcdf4->charmm==0.0.1) (1.6.4)
Requirement already satisfied: certifi in /home/pb777/miniforge3/envs/apo/lib/python3.11/site-packages (from netcdf4->charmm==0.0.1) (2025.1.31)
Requirement already satisfied: numpy in /home/pb777/miniforge3/envs/apo/lib/python3.11/site-packages (from netcdf4->charmm==0.0.1) (1.26.4)
Installing collected packages: charmm
DEPRECATION: Legacy editable install of charmm==0.0.1 from file:///home/pb777/apocharmm (setup.py develop) is deprecated. pip 25.1 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting in
@pgbarletta
pgbarletta / sh
Created September 22, 2024 14:32
swig error
# Configure with this line:
cmake -S. -Bbuild -DXTB_INCLUDE_DIR=/mnt/simdata/pbarletta/miniforge3/envs/mope/include -DXTB_LIBRARY_DIR=/mnt/simdata/pbarletta/miniforge3/envs/mope/lib -DCMAKE_INSTALL_PREFIX=/mnt/simdata/pbarletta/openmm-8.1.2 -DSWIG_EXECUTABLE=`which swig` -DCMAKE_PREFIX_PATH=/mnt/simdata/pbarletta/openmm-8.1.2
# go into build and compile+install
(mope) [yorkgroup@chardonnay build]$ make install
[ 11%] Building CXX object CMakeFiles/OpenMMXTB.dir/openmmapi/src/XtbForce.cpp.o
[ 22%] Building CXX object CMakeFiles/OpenMMXTB.dir/openmmapi/src/XtbForceImpl.cpp.o
[ 33%] Building CXX object CMakeFiles/OpenMMXTB.dir/serialization/src/XtbForceProxy.cpp.o
[ 44%] Building CXX object CMakeFiles/OpenMMXTB.dir/serialization/src/XtbSerializationProxyRegistration.cpp.o
@pgbarletta
pgbarletta / dodeca_mol.gro
Last active September 2, 2022 10:08
overlapping waters resSeq: 12090 and 17726
This file has been truncated, but you can view the full file.
Protein in water
106990
1MET N 1 7.653 8.044 2.968
1MET H1 2 7.655 8.055 2.867
1MET H2 3 7.611 8.127 3.008
1MET H3 4 7.749 8.037 2.999
1MET CA 5 7.577 7.924 3.006
1MET HA 6 7.623 7.837 2.959
1MET CB 7 7.577 7.898 3.158
1MET HB1 8 7.504 7.820 3.181
@pgbarletta
pgbarletta / a.pdb
Created June 15, 2022 12:30
small peptide example
ATOM 3242 N ALA B 1 49.830 33.030 25.480 1.00 0.00 N
ATOM 3243 H1 ALA B 1 50.530 32.320 25.620 1.00 0.00 H
ATOM 3244 H2 ALA B 1 49.230 32.900 24.680 1.00 0.00 H
ATOM 3245 H3 ALA B 1 50.280 33.940 25.390 1.00 0.00 H
ATOM 3246 CA ALA B 1 48.960 33.020 26.660 1.00 0.00 C
ATOM 3247 HA ALA B 1 49.210 32.120 27.230 1.00 0.00 H
ATOM 3248 CB ALA B 1 49.230 34.200 27.590 1.00 0.00 C
ATOM 3249 HB1 ALA B 1 48.530 34.040 28.410 1.00 0.00 H
ATOM 3250 HB2 ALA B 1 50.260 34.080 27.920 1.00 0.00 H
ATOM 3251 HB3 ALA B 1 49.060 35.140 27.080 1.00 0.00 H
@pgbarletta
pgbarletta / a.pdb
Created June 14, 2022 14:14
biobb_model
ATOM 3242 N ALA B 1 49.830 33.030 25.480 1.00 0.00 N
ATOM 3243 H1 ALA B 1 50.530 32.320 25.620 1.00 0.00 H
ATOM 3244 H2 ALA B 1 49.230 32.900 24.680 1.00 0.00 H
ATOM 3245 H3 ALA B 1 50.280 33.940 25.390 1.00 0.00 H
ATOM 3246 CA ALA B 1 48.960 33.020 26.660 1.00 0.00 C
ATOM 3247 HA ALA B 1 49.210 32.120 27.230 1.00 0.00 H
ATOM 3248 CB ALA B 1 49.230 34.200 27.590 1.00 0.00 C
ATOM 3249 HB1 ALA B 1 48.530 34.040 28.410 1.00 0.00 H
ATOM 3250 HB2 ALA B 1 50.260 34.080 27.920 1.00 0.00 H
ATOM 3251 HB3 ALA B 1 49.060 35.140 27.080 1.00 0.00 H
@pgbarletta
pgbarletta / result.jl
Created July 19, 2021 22:00
struct Result
profile::Any
score::Any
end
@pgbarletta
pgbarletta / gist:360040302c9874dc91b9356366f00c93
Created November 12, 2020 14:14
sample output
-6.9827E-03 -1.2060E-02 -3.3270E-03 5.5845E-03 -3.2249E-04 4.7521E-03 1.4404E-02 8.0357E-03 9.3137E-03 -9.2654E-03 5.0851E-03 -4.1534E-03 8.0331E-03 -1.8683E-02 -3.0116E-03 -1.7126E-02 4.6249E-03 4.3449E-04 3.4349E-03 4.7597E-03 -1.9952E-02 -1.4510E-02 1.9948E-02 -1.1514E-02 5.2085E-04 1.2077E-02 -2.7057E-03 6.2760E-03 -1.5432E-02 2.1348E-02
-1.0917E-02 -1.8234E-02 -1.0469E-02 1.2871E-03 -9.4562E-03 1.7884E-02 1.7945E-02 3.8684E-03 1.5073E-02 -6.8396E-03 1.7008E-02 5.2361E-03 7.9040E-03 -3.3773E-03 3.0501E-03 8.9497E-03 -1.7244E-03 -2.3878E-03 2.3819E-03 -1.0553E-02 1.9088E-02 -9.6169E-03 -2.7147E-03 -2.7411E-03 -4.7664E-03 9.2445E-05 -7.8470E-03 3.2568E-03 -1.0433E-02 -1.3052E-02
@pgbarletta
pgbarletta / gist:4c5d8a540379ce5d321fad3c09470948
Created November 12, 2020 14:08
sample fixed with file
-6.9827E-03 -1.2060E-02 -3.3270E-03 5.5845E-03 -3.2249E-04 4.7521E-03 1.4404E-02 8.0357E-03 9.3137E-03 -9.2654E-03 5.0851E-03 -4.1534E-03 8.0331E-03 -1.8683E-02 -3.0116E-03 -1.7126E-02 4.6249E-03 4.3449E-04 3.4349E-03 4.7597E-03 -1.9952E-02 -1.4510E-02 1.9948E-02 -1.1514E-02 5.2085E-04 1.2077E-02 -2.7057E-03 6.2760E-03 -1.5432E-02 2.1348E-02
-1.0917E-02 -1.8234E-02 -1.0469E-02 1.2871E-03 -9.4562E-03 1.7884E-02 1.7945E-02 3.8684E-03 1.5073E-02 -6.8396E-03 1.7008E-02 5.2361E-03 7.9040E-03 -3.3773E-03 3.0501E-03 8.9497E-03 -1.7244E-03 -2.3878E-03 2.3819E-03 -1.0553E-02 1.9088E-02 -9.6169E-03 -2.7147E-03 -2.7411E-03 -4.7664E-03 9.2445E-05 -7.8470E-03 3.2568E-03 -1.0433E-02 -1.3052E-02
6.4556E-03 6.5247E-03 7.8063E-03 -8.7517E-03 -2.4766E-03 -7.2918E-04 -4.7568E-03 1.6271E-02 2.9609E-03 -9.9944E-03 1.6501E-02 3.1646E-03 5.3735E-03
@pgbarletta
pgbarletta / CMakeCache.txt
Created August 21, 2020 19:41
CMakeCache
# This is the CMakeCache file.
# For build in directory: /home/pbarletta/amber20_src/build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
@pgbarletta
pgbarletta / config.h
Created August 20, 2020 23:59
configure
# Compatibility config.h generated by the CMake build system
###############################################################################
# (1) Location of the installation
BASEDIR=/usr/local/amber20_src/build
AMBER_PREFIX=/usr/local/amber20//
BINDIR=$(AMBER_PREFIX)/bin