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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/ .

Info

It is recommended currently to use Schrodinger through an interactive session because of some issues encountered when submitting jobs through submission scripts.

Start an interactive session:

Code Block
srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash
Info

Make sure to include the “--x11” flag for the GUI

Load Modules

Code Block
module load schrodinger/20222023-43

You can then see a list of executable programs:

Code Block
find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/20222023-43/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t
autots    desmond   gfxinfo   jsc       material  phase_hy  qiksim    ska biolumin  elements  glidehppmap    knime jws       mxmd      phase_qs  qpld      sspska
blast biolumin    epik      hppmapifd    knime   lambda_d  oned_scr  phase_sc  qsite     stassp
bminblast      epikx     ifd   -md    licadmin  para_tes  pipeline  runquick_sh  sta
bmin    structur confgen   fep_abso  ifd-mdimpact    ligand_s  pfam      prime     run schrodin      testappstructur
confgen confgenx  fep_plus  impactinstalla    ligprep   phase_bu  prime_mm  shape_scschrodin  vswtestapp
consensuconfgenx  fep_solu  installajaguar    machid    phase_da  primex    shape_sc  watermapvsw
constantconsensu  ffbuilde  jaguarjobcontr    macromod  phase_fi  qikfit    shape_sc  wscorewatermap
covalentconstant  generate  jsc    jobcontr   maestro   phase_fq  qikprop   shape_sc  wscore
covalent  gfxinfo   jws       material  phase_hy  qiksim    sitemap   xtb
desmond   glide

You can also see a list of utilities with the same find command above:

Code Block
find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/20222023-43/utilities/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t
2d_sketc  canvasHC  cg_chsr ccp42cns  create_xw  jnannyjaguar_p    neutralimtzprint  project_  store_restructal
abs       canvasHC  cgcheck_chsrjo   create_x  jobcontrjaguar_t  numfreqcmultisim  project_  structalstructca
align_bi  canvasJocanvasKM  check_jore  create_x  jaguar_t  neutrali  project_  structco
align_hy  canvasKP   jserver check_th  create_x  jnanny  obabel  numfreqc  propfilt  structcastructsh
align_hyli  canvasKMcanvasLC  checkch_thisost  custom_p  jserver_jobcontr  obabel  para_bmi  proplist  structcostructsu
align_lianharmon  canvasKPcanvasLi  ch_isostligan  desalter  lictest jresults  para_epibmi  protassi  structur
apbs   structsh anharmon  canvasLCcanvas_m  ch_liganwater  elim.sch  licutiljserver   para_ligepi  py.test   structurstu_add
apbsapplyhtr  canvasMC    canvasLi  ch_watercluster_  epharmac  ligandjserver_i  pathpara_finlig  query_gp  stu_adddele
applyhtrautoqsar  canvas_mcanvasMD  cluster_combinat  extract_  lictest ligfilte  pbspath_lic_fin  queue_bm  stu_deleexec
autoqsarAutoTSRe  canvasMCcanvasML  combinat  feature_  ligparselicutil   pdbconvepbs_lic_  randsub   stu_execextr
AutoTSRe  canvasMDcanvasMo  combinat  feature_  lpligand_filtei  phase_alpdbconve  refconve  stu_extrmodi
AutoTSRe  canvasMLcanvasNn  combinat  ffld_ser  lp_labelligfilte  phase_clal  render_k  stu_modiwork
AutoTSReAutoTSUn  canvasMocanvasPC  combinatcompare_  flex_ali  lp_noredligparse  phase_cocl  r_group_  stusystem_workb
babel     canvasNncanvasPC  compare_configur  flexlm_s  macrolp_pkfilte  phase_co  r_group_  system_btautomer
bandshap  canvasPC  configurconf_tem  fragment  maegearslp_label  phase_deco  ring_con  tautomerthermoch
buildloo  canvasPC  confconvert_tem  generate  maesubselp_nored  phase_hyde  ring_tem  thermochtimestam
canvas_acanvasBa  canvasPCcanvasPh  convert_  generate  maetopqrmacro_pk  phase_hy  rmsdcalc  timestamuffmin
canvasBacanvasCo  canvasPCcanvasPL  convert_  getpdb    mae_to_smaegears  phase_hy  rsync_pd  uffminunique_n
canvasCocanvasCS  canvasPhcanvasPr  convert_  glide_en  makejbasmaetopqr  phase_mmhy  sdconver  unique_nuniquesm
canvasCS  canvasPLcanvasPW  convert_corefind  glide_me  makemae_to_lins  phase_prmm  sdsubsetsecstruc  uniquesmupdate_B
canvasCS  canvasPrcanvasRP  corefindcreate_h  glide_so  make_r_llin  phase_qspr  secstrucseqconve  update_BP
canvasCScanvasDB  canvasPWcanvasSc  create_h  guardian  md5digesmake_r_l  phase_voqs  seqconveserial_s  vis2gc
canvasDBcanvasFP  canvasRPcanvasSD  create_h  hetgrp_f  merge_dumd5diges  postmortphase_vo  serialshape_ssc  visdump
canvasFP  canvasSccanvasSe  create_h  hit_expa  micromerge_pkdu  preminpostmort    shapeshow_scjoi  watermap
canvasFP  canvasSDcanvasSO  create_hi  impref    mol2convmicro_pk  premin  prepwiza  showsmiles_joit  wscore_m
canvasFP  canvasSecanvasSO  create_im  ionizer   moldescrmodify_s  profile_prepwiza  smiles_tspectrum  wscore_r
canvasFP  canvasSOcanvasTr  create_mr  ionizer_  mtzprintmol2conv  profile_  spectrumstereoiz  zip_temp
canvasFPcanvasHC  canvasSOccp42cns  create_s  jagconve  multisimmoldescr  projectprofile_  stereoizstore_re  ziputil
canvasHC  canvasTr  create_w  jaguar_p

Example Application Usage

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