packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen/data/solvent.parm

@@ -0,0 +1,14 @@
+#DEN TFE                                 sigmaaldrich
+#DEN ETOH MEOH DMSO ACT ACN BNZ TOL CLO  PubChem
+#Solvent        Density[g/cm3] MolecularWeight[g/mol]   Charge    Name                          ParamSource
+WAT             0.997                18                   0       Water                         "-"
+DMS             1.100                78                   0       Dimethylsulfoxide             "Strader_&_Feller_10.1021/jp013658n"
+TFE             1.38                100                   0       2,2,2-Trifluoroethanol        "Vymetal_&_Vondrasek_10.1021/jp505861b"
+ACN             0.79                 41                   0       Acetonitrile                  "Nikitin_&_Lyubartsev_10.1002/jcc.20721"
+MOH             0.79                 32                   0       Methanol                      "Cieplak_et._al_10.1002/jcc.1065"
+CL3             1.48                119                   0       Chloroform                    "Cieplak_et._al_10.1002/jcc.1065"
+NMA             0.94                 73                   0       N-Methylacetamide             "Cieplak_et._al_10.1002/jcc.1065"
+ACT             0.79                 58                   0       Acetone                       "OPLS-NB_+_AMBER_Lexa_et._al_10.1021/ci400741u"
+BNZ             0.88                 78                   0       Benzene                       "OPLS-NB_+_AMBER_Lexa_et._al_10.1021/ci400741u"
+IPH             1.04                 94                   0       Phenol                        "OPLS-NB_+_AMBER_Lexa_et._al_10.1021/ci400741u"
+siWT4           0.997               198                   0       Sirah_Water                   "-"

packmol_memgen/example/example.sh

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+#!/bin/bash
+#
+#PACKMOL MEMGEN EXAMPLE
+#
+#This example run is for the Streptomyces Potassium Channel KcsA. This will protonate
+#and orientate the protein, and prepare a membrane system with a DOPE:DOPG mixture 3:1.
+
+if [[ $1 = "clean" ]]; then
+cd $(dirname $0)
+#rm $(ls -I example.sh)
+find . \! -name "example.sh" -type f -delete
+exit
+fi
+
+SCRIPT_PATH=../main.py
+
+PDB=1BL8
+
+if [[ ! -f ${PDB}.pdb ]]; then
+    echo "DOWNLOADING PDB FILE..."
+    wget https://files.rcsb.org/download/${PDB}.pdb
+fi
+
+echo "RUNNING PACKMOL_MEMGEN..."
+
+if [[ $1 = "test" ]]; then
+$SCRIPT_PATH --pdb ${PDB}.pdb --lipids DOPE:DOPG --ratio 3:1 --salt_c K+ --keep --nloop 2 --nloop_all 2 --plot --mem_opt 2 --writeout 2
+exit
+fi
+
+$SCRIPT_PATH --pdb ${PDB}.pdb --lipids DOPE:DOPG --ratio 3:1 --salt_c K+ --plot

packmol_memgen/lib/amber.py

@@ -0,0 +1,77 @@
+#! /usr/bin/python
+
+from __future__ import print_function
+import os 
+import logging
+
+logger = logging.getLogger("pmmg_log")
+
+if os.name == 'nt':
+    exe_suffix =    ".exe"
+else: 
+    exe_suffix =    ""
+
+amber_ion_dict = {
+"NH4+" :( "NH4" ,  1,"NH4" ),
+"H3O+" :( "H3O+",  1,"H3O+"),
+"Li+"  :(  "LI" ,  1, "LI" ),#   3  
+"Be2+" :(  "Be" ,  2, "Be" ),#   4  
+"F-"   :(  "F"  , -1, "F"  ),#   9  
+"Na+"  :(  "Na+",  1, "Na+"),#   11 
+"Mg2+" :(  "MG" ,  2, "MG" ),#   12 
+"Al3+" :(  "AL" ,  3, "AL" ),#   13 
+"Cl-"  :(  "Cl-", -1, "Cl-"),#   17 
+"K+"   :(  "K+" ,  1, "K+" ),#   19 
+"Ca2+" :(  "CA" ,  2, "CA" ),#   20 
+"V2+"  :(  "V2+",  2, "V2+"),#   23 
+"Cr2+" :(  "Cr" ,  2, "Cr" ),#   24 
+"Cr3+" :(  "CR" ,  3, "CR" ),#   24 
+"Mn2+" :(  "MN" ,  2, "MN" ),#   25 
+"Fe2+" :(  "FE2",  2, "FE2"),#   26 
+"Fe3+" :(  "FE" ,  3, "FE" ),#   26 
+"Co2+" :(  "CO" ,  2, "CO" ),#   27 
+"Ni2+" :(  "NI" ,  2, "NI" ),#   28 
+"Cu+"  :(  "CU1",  1, "CU1"),#   29 
+"Cu2+" :(  "CU" ,  2, "CU" ),#   29 
+"Zn2+" :(  "ZN" ,  2, "ZN" ),#   30 
+"Br-"  :(  "BR" , -1, "BR" ),#   35 
+"Rb+"  :(  "RB" ,  1, "RB" ),#   37 
+"Sr2+" :(  "SR" ,  2, "SR" ),#   38 
+"Y3+"  :(  "Y"  ,  3, "Y"  ),#   39 
+"Zr4+" :(  "Zr" ,  4, "Zr" ),#   40 
+"Pd2+" :(  "PD" ,  2, "PD" ),#   46 
+"Ag+"  :(  "AG" ,  1, "AG" ),#   47 
+"Ag2+" :(  "Ag" ,  2, "Ag" ),#   47 
+"Cd2+" :(  "CD" ,  2, "CD" ),#   48 
+"In3+" :(  "IN" ,  3, "IN" ),#   49 
+"Sn2+" :(  "Sn" ,  2, "Sn" ),#   50 
+"I-"   :(  "IOD", -1, "IOD"),#   53 
+"Cs+"  :(  "CS" ,  1, "CS" ),#   55 
+"Ba2+" :(  "BA" ,  2, "BA" ),#   56 
+"La3+" :(  "LA" ,  3, "LA" ),#   57 
+"Ce3+" :(  "CE" ,  3, "CE" ),#   58 
+"Ce4+" :(  "Ce" ,  4, "Ce" ),#   58 
+"Pr3+" :(  "PR" ,  3, "PR" ),#   59 
+"Nd3+" :(  "Nd" ,  3, "Nd" ),#   60 
+"Sm2+" :(  "Sm" ,  2, "Sm" ),#   62 
+"Sm3+" :(  "SM" ,  3, "SM" ),#   62 
+"Eu3+" :(  "EU3",  3, "EU3"),#   63 
+"Eu2+" :(  "EU" ,  2, "EU" ),#   63 
+"Gd3+" :(  "GD3",  3, "GD3"),#   64 
+"Tb3+" :(  "TB" ,  3, "TB" ),#   65 
+"Dy3+" :(  "Dy" ,  3, "Dy" ),#   66 
+"Er3+" :(  "Er" ,  3, "Er" ),#   68 
+"Tm3+" :(  "Tm" ,  3, "Tm" ),#   69 
+"Yb2+" :(  "YB2",  2, "YB2"),#   70 
+"Lu3+" :(  "LU" ,  3, "LU" ),#   71 
+"Hf4+" :(  "Hf" ,  4, "Hf" ),#   72 
+"Pt2+" :(  "PT" ,  2, "PT" ),#   78 
+"Hg2+" :(  "HG" ,  2, "HG" ),#   80 
+"Tl+"  :(  "TL" ,  1, "TL" ),#   81 
+"Tl3+" :(  "Tl" ,  3, "Tl" ),#   81 
+"Pb2+" :(  "PB" ,  2, "PB" ),#   82 
+"Ra2+" :(  "Ra" ,  2, "Ra" ),#   88 
+"Th4+" :(  "Th" ,  4, "Th" ),#   90 
+"U4+"  :(  "U4+",  4, "U4+"),#   92 
+"Pu4+" :(  "Pu" ,  4, "Pu" )#   94 
+}