--- title: "Schrödinger" canonical: "https://kb.uconn.edu/space/SH/26033816477/Schr%C3%B6dinger" format: markdown --- The Schrödinger Suite is a collection of software for chemical and biochemical use. It offers various tools that facilitate the investigation of the structures, reactivity and properties of chemical systems. There is a campus site license for this software, supported by UITS. More information is available here: [http://software.uconn.edu/schrodinger/](http://software.uconn.edu/schrodinger/) . > ℹ️ It is recommended currently to use Schrodinger through an **interactive session** because of some issues encountered when submitting jobs through submission scripts. > 📝 Maestro does not work well on HPC due to needing to spawn a job server, it is recommend to run the main Maestro simulation on a local PC or local lab machine then port the simulation over to HPC and run the other Schrodinger commands through the command line. # Start an interactive session: ``` srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash ``` > ℹ️ Make sure to include the “--x11” flag for the GUI # Load Modules Once a node is assigned to the interactive srun job in the previous section, schrodinger can be loaded from one of the various modules available on HPC. ``` module load schrodinger/2025-4 ``` You can then see a list of executable programs: ``` find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2025-4/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t autots desmond glide jsc material phase_hy qikprop ska biolumin epik glide_ws jws mxmd phase_qs qiksim ssp blast epikx hppmap knime oned_scr phase_sc qsite sta bmin fep_abso ifd licadmin para_tes pipeline quick_sh structur confgen fep_plus ifd-md ligand_s pfam ppi_md_s run testapp confgenx fep_resi impact ligprep phase_bu prime shape_sc unbindin consensu fep_solu installa machid phase_da prime_mm shape_sc vsw constant ffbuilde jaguar macromod phase_fi primex shape_sc watermap covalent generate jobcontr maestro phase_fq qikfit sitemap xtb crystal_ gfxinfo ``` You can also see a list of utilities with the same find command above: ``` find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2025-4/utilities/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t 2d_sketc canvasHC cg_chsr create_w ionizer_ moldescr project_ structal abs canvasHC check_jo create_x jagconve mtzprint project_ structca align_bi canvasKM check_re create_x jaguar_p multisim propfilt structco align_hy canvasKP check_th create_x jaguar_t neutrali proplist structsh align_li canvasLC ch_isost custom_p jaguar_t obabel protassi structsu anharmon canvasLi ch_ligan desalter jnanny para_bmi py.test structur apbs canvas_m ch_water elim.sch jobcontr para_epi query_gp stu_add applyhtr canvasMC cluster_ epharmac jresults path_fin queue_bm stu_dele autoqsar canvasMD combinat extract_ jserver pbs_lic_ randsub stu_exec AutoTSRe canvasML combinat feature_ jserver_ pdbconve refconve stu_extr AutoTSRe canvasMo combinat feature_ lictest phase_al render_k stu_modi AutoTSRe canvasNn combinat ffld_ser licutil phase_cl r_group_ stu_work AutoTSUn canvasPC compare_ flex_ali ligfilte phase_co r_group_ system_b bandshap canvasPC configur flexlm_s ligparse phase_co ring_con tautomer bb_datab canvasPC conf_tem fragment lp_filte phase_de ring_tem thermoch buildloo canvasPC convert_ generate lp_label phase_hy rmsdcalc timestam canvasBa canvasPh convert_ generate lp_nored phase_hy rsync_pd unique_n canvasCo canvasPL convert_ getpdb macro_pk phase_hy sdconver uniquesm canvasCS canvasPr convert_ glide_en maegears phase_mm secstruc update_B canvasCS canvasPW corefind glide_me maetopqr phase_pr seqconve update_P canvasCS canvasRP create_h glide_so mae_to_s phase_qs serial_s vis2gc canvasDB canvasSc create_h glide_ws make_lin phase_vo shape_sc visdump canvasFP canvasSD create_h glide_ws make_r_l postmort show_joi watermap canvasFP canvasSe create_h guardian md5diges premin smiles_t wscore_m canvasFP canvasSO create_i hetgrp_f merge_du prepwiza spectrum wscore_r canvasFP canvasSO create_m hit_expa micro_pk profile_ stereoiz zip_temp canvasFP canvasTr create_r impref modify_s profile_ store_re ziputil canvasHC ccp42cns create_s ionizer mol2conv project_ ``` # Example Application Usage ## qsite ``` qsite -SAVE -PARALLEL 24 3IIS_Per1.in ``` Note that the numeric value of `-PARALLEL` should match the numeric value of the `-n declaration` that you specified in the previous srun command. ## Jaguar ``` jaguar run nameofinput.in ``` There is a way to target a specific Schrodinger application or utility with the following syntax: You can then view the status of your running job with `sacct`. ``` sacct JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 39148 j3IIS_Per1 hi-core abc12345 24 RUNNING 0:0 391148.0 hostname abc12345 24 COMPLETED 0:0 ``` ## Run Test Suite ``` testapp -DEBUG para_testapp -DEBUG ``` ## Installation Oddities Schrödinger comes pre-packaged with an outdated version of mpi(< 1.8.1), meaning an old bug in the MPI->SLURM interface needs to be manually patched by appending the following line to schrodinger's mpi's default config file: ``` plm_slurm_args = --cpu_bind=boards ``` ## Command to call a Schrodinger utility ``` "${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_TREK1model_1ms restOfCommandOptionsHere ``` ## Launching and disconnecting from an interactive srun Schrodinger job Schrodinger can be run interactively through srun. The srun solution above is good for a single interactive calculation that can be left up and running without any disconnections. If there are network or power interruptions while the Interactive Schrodinger srun job is running, the srun job will end and progress will be lost. Here is an example to allocate an AMD EPYC compute node with 126 cores through srun under the general partition: ``` srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash ``` Once a compute node is assigned and the srun job is running, schrodinger can be loaded normally through the module. ``` module load schrodinger/2026-2 ``` Once schrodinger is loaded, the Schrodinger commands will become available and the Schrodinger calculations can be called through one of the many Schrodinger suites. ## Example Schrodinger submission script: (piper process): The following example is a general overview how a job for Schrodinger can be used to run simulations. Replace the piper command with the designated Schrodinger command needed for the calculation. ```shell #!/bin/bash #SBATCH --job-name=prot-prot-docking_AR_1 #SBATCH --partition=general #SBATCH --ntasks=40 #SBATCH --time=12:00:00 #SBATCH --mail-type=END #SBATCH --mail-user=first.lastname@uconn.edu #SBATCH --error=Protein-Protein-docking_%j.err #SBATCH --output=Protein-Protein-docking_%j.out module purge module load schrodinger/2026-2 export SCHRODINGER=/gpfs/software/RHEL9/schrodinger/2026-2 mkdir -pv $HOME/schrodinger_tmp #remove this from submission after the schrodinger_tmp directory gets created export SCHRODINGER_TMPDIR=$HOME/schrodinger_tmp $SCHRODINGER/jsc local-server-start "${SCHRODINGER}/run" -FROM psp piper.py \ -jobname NameofJOb \ -receptor file.pdb \ -receptor_chain B \ -poses NumberofPoses \ -rotations numberOfRotations \ -raw \ -OMPI $SLURM_NTASKS \ -ligand nameOfLigand.pdb \ -ligand_chain A \ -use_nonstandard_residue yes \ -HOST localhost:$SLURM_NTASKS \ -WAIT \ -TMPLAUNCHDIR $SCHRODINGER/jsc local-server-stop ``` ## Example Schrodinger submission script: (desmond): ```shell #!/bin/bash #SBATCH --job-name=desmond #SBATCH --nodes=1 #SBATCH --ntasks=126 #SBATCH --partition=general #SBATCH --mail-type=END #SBATCH --mail-user=first.lastname@uconn.edu #SBATCH --error=JobTest.err #SBATCH --output=JobTest.out module purge module load schrodinger/2026-2 export SCHRODINGER=/gpfs/software/RHEL9/schrodinger/2026-2 mkdir -pv $HOME/schrodinger_tmp #remove this from submission after the schrodinger_tmp directory gets created export SCHRODINGER_TMPDIR=$HOME/schrodinger_tmp $SCHRODINGER/jsc local-server-start $SCHRODINGER/desmond \ -LOCAL \ -WAIT \ -HOST localhost:$SLURM_NTASKS \ -c job.cfg \ -in system.cms -TMPLAUNCHDIR $SCHRODINGER/jsc local-server-stop ```