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Tinker: Software Tools for Molecular Design
https://dasher.wustl.edu/tinker/
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about tinker toturials #146

Closed Cynthia-0807 closed 10 months ago

Cynthia-0807 commented 11 months ago

two website about tinker toturials cannot be opened: https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut https://sites.google.com/site/biomolsimstw/workshop-materials/tutorials

pren commented 11 months ago

FYI: https://github.com/TinkerTools/tinker-openmm [https://opengraph.githubassets.com/576476bd3fc6a93102b10b133c638c97c3020ca691726013de48065bc606faf9/TinkerTools/tinker-openmm]https://github.com/TinkerTools/tinker-openmm GitHub - TinkerTools/tinker-openmm: Tinker-OpenMM: Tinker Interface for OpenMMhttps://github.com/TinkerTools/tinker-openmm Tinker-OpenMM: Tinker Interface for OpenMM. Contribute to TinkerTools/tinker-openmm development by creating an account on GitHub. github.com

From: Yiqiu Wang @.> Sent: Tuesday, October 31, 2023 8:50 PM To: TinkerTools/tinker @.> Cc: Subscribed @.***> Subject: [TinkerTools/tinker] error occurred when compiling tinker-openmm (Issue #146)

When I used the command make -j to compile tinker-openmm, the error was reported:

ommdata.f:158:63:

   call set_polar_data (npolar,ipolar,polarity,thole,dirdamp,pdamp,
                                                           1

Error: Symbol ‘dirdamp’ at (1) has no IMPLICIT type; did you mean ‘pdamp’? ommdata.f:169:49:

  &                      w4scale,w5scale,udiag,polprt,dpequal,
                                             1

Error: Symbol ‘udiag’ at (1) has no IMPLICIT type; did you mean ‘udirp’? ommdata.f:170:49:

  &                      use_thole,use_dirdamp,poltyp)
                                             1

Error: Symbol ‘use_dirdamp’ at (1) has no IMPLICIT type; did you mean ‘use_disp’? ommdata.f:174:68:

  &                      use_angtor,use_tortor,use_vdw,use_repuls,
                                                                1

Error: Symbol ‘use_repuls’ at (1) has no IMPLICIT type; did you mean ‘use_repel’? make: [ommdata.o] Error 1 make: Waiting for unfinished jobs....

Why? My install environment is above:

TINKERDIR = $(HOME)/software/tinker-openmm TINKER_LIBDIR = $(TINKERDIR)/lib BINDIR = $(TINKERDIR)/bin LINKDIR = /usr/local/bin

FFTWDIR = $(HOME)/software/tinker/fftw FFTW_LIBDIR = -L$(FFTWDIR)/lib FFTW_LIBS = -lfftw3_threads -lfftw3

OPENMMDIR = $(HOME)/software/openmm-7.5.0 OPENMM_INCLUDE = $(OPENMMDIR)/include OPENMM_LIBDIR = -L$(OPENMMDIR)/lib OPENMM_LIBS = -lOpenMM -lOpenMMAmoeba

CUDA_DIR = $(HOME)/software/cuda-11.4.1 CUDA_INCLUDE = $(CUDA_DIR)/include CUDA_LIB = $(CUDA_DIR)/lib

Uncomment below for 64-bit Linux only

CUDA_LIB = $(CUDA_DIR)/lib64 NVML_INCLUDE = $(CUDA_DIR)/include NVML_LIB = $(CUDA_DIR)/lib64/stubs

Moreover,two website about tinker toturials cannot be opened: https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut https://sites.google.com/site/biomolsimstw/workshop-materials/tutorials

— Reply to this email directly, view it on GitHubhttps://github.com/TinkerTools/tinker/issues/146, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNC6XXJR4O2RR3BWGXEEV3YCGTHFAVCNFSM6AAAAAA6YTBIC2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3TCNJVGAYDOOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Cynthia-0807 commented 11 months ago

Thanks for your reply.I have read this link before installing tinker-openmm,so I install openmm-7.5.0(it was released in Dec 10, 2020, prior to 4 march 2021). I will try older version.

FYI: https://github.com/TinkerTools/tinker-openmm [https://opengraph.githubassets.com/576476bd3fc6a93102b10b133c638c97c3020ca691726013de48065bc606faf9/TinkerTools/tinker-openmm]https://github.com/TinkerTools/tinker-openmm GitHub - TinkerTools/tinker-openmm: Tinker-OpenMM: Tinker Interface for OpenMMhttps://github.com/TinkerTools/tinker-openmm Tinker-OpenMM: Tinker Interface for OpenMM. Contribute to TinkerTools/tinker-openmm development by creating an account on GitHub. github.com … ____ From: Yiqiu Wang @.> Sent: Tuesday, October 31, 2023 8:50 PM To: TinkerTools/tinker @.> Cc: Subscribed @.> Subject: [TinkerTools/tinker] error occurred when compiling tinker-openmm (Issue #146) When I used the command make -j to compile tinker-openmm, the error was reported: ommdata.f:158:63: call set_polar_data (npolar,ipolar,polarity,thole,dirdamp,pdamp, 1 Error: Symbol ‘dirdamp’ at (1) has no IMPLICIT type; did you mean ‘pdamp’? ommdata.f:169:49: & w4scale,w5scale,udiag,polprt,dpequal, 1 Error: Symbol ‘udiag’ at (1) has no IMPLICIT type; did you mean ‘udirp’? ommdata.f:170:49: & use_thole,use_dirdamp,poltyp) 1 Error: Symbol ‘use_dirdamp’ at (1) has no IMPLICIT type; did you mean ‘use_disp’? ommdata.f:174:68: & use_angtor,use_tortor,use_vdw,use_repuls, 1 Error: Symbol ‘use_repuls’ at (1) has no IMPLICIT type; did you mean ‘use_repel’? make: [ommdata.o] Error 1 make: Waiting for unfinished jobs.... Why? My install environment is above: TINKERDIR = $(HOME)/software/tinker-openmm TINKER_LIBDIR = $(TINKERDIR)/lib BINDIR = $(TINKERDIR)/bin LINKDIR = /usr/local/bin FFTWDIR = $(HOME)/software/tinker/fftw FFTW_LIBDIR = -L$(FFTWDIR)/lib FFTW_LIBS = -lfftw3_threads -lfftw3 OPENMMDIR = $(HOME)/software/openmm-7.5.0 OPENMM_INCLUDE = $(OPENMMDIR)/include OPENMM_LIBDIR = -L$(OPENMMDIR)/lib OPENMM_LIBS = -lOpenMM -lOpenMMAmoeba CUDA_DIR = $(HOME)/software/cuda-11.4.1 CUDA_INCLUDE = $(CUDA_DIR)/include CUDA_LIB = $(CUDA_DIR)/lib # Uncomment below for 64-bit Linux only CUDA_LIB = $(CUDA_DIR)/lib64 NVML_INCLUDE = $(CUDA_DIR)/include NVML_LIB = $(CUDA_DIR)/lib64/stubs Moreover,two website about tinker toturials cannot be opened: https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut https://sites.google.com/site/biomolsimstw/workshop-materials/tutorials — Reply to this email directly, view it on GitHub<#146>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNC6XXJR4O2RR3BWGXEEV3YCGTHFAVCNFSM6AAAAAA6YTBIC2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3TCNJVGAYDOOA. You are receiving this because you are subscribed to this thread.Message ID: @.>