![]() P_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c \Ĭhk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c \ P_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c \ Molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c \ Hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c \ Thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c \ SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c \ LDFLAGS = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm CC = icc -O3 -static -ipo -xSSE2 -no-prec-div -pthread -I$(MKLROOT)/include Makefiles are sensitive to whitespace - there is a difference between TAB and SPACE. IMPORTANT you cannot just copy and paste this. ![]() We use the version of STRIDE archived by the VMD team.Įdit the file stride.h, and change line 43 to:Īlso, edit stride.c, and change line 96 from "return(SUCCESS) " to:Ĭreate your own makefile named ac. VMD depends on several external programs, some of which have to be compiled. In general, we will redirect all make output to a file so that any error messages will be captured and not scroll off the screen. This creates two directories: vmd-1.9.1 and plugins. Set up your environment to use the Intel compilers:Įxport VMDHOME ~/Applications/vmd-1.9.1 # tcsh: setenv VMDHOME ~/Applications/vmd-1.9.1Ĭreate a directory to contain all the VMD-related source code:Įxport VMDSRCDIR=~/src/vmd # this is for bash for tcsh/csh, do "setenv VMDSRCDIR ~src/vmd"ĭownload and expand the source code in that directory: Here is a non-exhaustive list of prerequisite packages (as provided by RedHat):įirst, read the official compilation guide. Neither is required but will greatly speed up execution. If an NVIDIA graphics card is installed, and if the CUDA GPU programming software development kit is installed, it can take advantage of both. It requires 3D graphics libraries (OpenGL, MESA) to function. The source code is available at the VMD website. Currently installed on the cluster is version 1.9.1.
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