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

packmol_memgen/data/frcmod.lipid_ext

@@ -0,0 +1,97 @@
+AMBER Lipid Force Field Extension BETA / Inclusion of PI and LysoPL S. Schott-Verdugo, H. Gohlke
+MASS
+cE 12.01      GAFF2 ce
+
+BOND
+cE-cE  306.1    1.4570      ce-ce GAFF2
+cB-cE  460.5    1.3460      cb-ce GAFF2
+cE-hB  391.4    1.0880      ce-ha GAFF2
+cA-Os  337.00   1.450       CT-Os GLYCAM06j
+Cp-Cp  310.00   1.520       Cg-Cg GLYCAM06j
+P -oH  230.00   1.610       oH-pA lipid17
+
+ANGLE
+cA-cB-cE    66.1      123.15    c3-c2-ce GAFF2
+cB-cE-hB    50.1      119.94    c2-ce-ha GAFF2
+cB-cE-cE    67.5      123.26    c2-ce-ce GAFF2
+cE-cE-hB    47.7      116.65    ce-ce-ha GAFF2
+cB-cD-cA    65.5      111.56    c2-c3-c3 GAFF2
+cA-cA-Os   67.78      108.42    lipid17 // Lipid11 v1.0  (GAFF c3-c3-os)
+cA-Os-P   100.00      120.50    lipid17 // Lipid17 v1.0  (parm99 CT-OS-P)
+hE-cA-Os   50.84      108.82    lipid17 // Lipid11 v1.0  (GAFF h1-c3-os)
+Cp-Cg-Cp   45.00      113.50    GLYCAM06j // Propane
+Cp-Cg-Oh   70.00      107.50    GLYCAM06j // Ethanol
+Cg-Cp-Cp   45.00      113.50    GLYCAM06j // Propane
+Cp-Cp-H1   45.00      111.00    GLYCAM06j // Propanol
+Cp-Cp-Cp   45.00      113.50    GLYCAM06j // Propane
+Cp-Cp-Os   70.00      107.50    GLYCAM06j // Ethanol
+Os-P -oH   90.0       108.23    O2-P -OH Modified DOI: 10.1021/ct300613v
+P -oH-hO   100.0      113.28    HO-OH-P  Modified DOI: 10.1021/ct300613v
+oH-P -O2   90.0       108.23    O2-P -OH Modified DOI: 10.1021/ct300613v
+
+DIHE
+X -cB-cE-X    4        26.600          180.000          2.000   X -c2-ce-X GAFF2
+cB-cE-cE-cB   1         0.500          180.000          2       c2-ce-ce-c2 GAFF2
+X -cE-cE-X    4         4.000          180.000          2.000   X -ce-ce-X GAFF2
+cB-cA-cA-cB   9         1.400            0.000          3.000   X -c3-c3-X GAFF2
+hA-cA-cD-cB   9         1.400            0.000          3.000   X -c3-c3-X GAFF2
+cA-cA-cD-cB   9         1.400            0.000          3.000   X -c3-c3-X GAFF2
+cE-cB-cA-hA   6         0.000            0.000          2.000   X -c2-c3-X GAFF2
+cE-cB-cA-cA   6         0.000            0.000          2.000   X -c2-c3-X GAFF2
+hB-cB-cD-cA   6         0.000            0.000          2.000   X -c2-c3-X GAFF2
+cB-cB-cD-cA   6         0.000            0.000          2.000   X -c2-c3-X GAFF2
+oH-cA-cA-oS   1         0.1440           0.00          -3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF oh-c3-c3-oh) for Lyso
+oH-cA-cA-oS   1         1.1750           0.00           2.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF oh-c3-c3-oh) for Lyso
+cA-cA-cA-Os   1         0.1556           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF X -c3-c3-X )
+cA-cA-Os-P    3         1.1500           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid17 v1.0  (parm99 X -CT-OS-X )
+hE-cA-cA-Os   1         0.0000           0.00          -3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF h1-c3-c3-os)
+              1         0.2500           0.00           1.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF h1-c3-c3-os)
+cA-Os-P -Os   1         0.2500           0.00          -3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid17 v1.1  (parm99 OS-P -OS-CT)
+              1         1.2000           0.00           2.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid17 v1.1  (parm99 OS-P -OS-CT)
+cA-Os-P -O2   3         0.7500           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid17 v1.0  (parm99 X -OS-P -X )
+hE-cA-Os-P    3         1.1500           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid17 v1.0  (parm99 X -CT-OS-X )
+Os-cA-cA-oS   1         0.1440           0.00          -3.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF os-c3-c3-os)
+              1         1.1750           0.00           2.00    SCEE=1.2 SCNB=2.0     lipid17 // Lipid11 v1.0  (GAFF os-c3-c3-os)
+Os-Cp-Cg-Cp   1        -0.27             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Cg 1-methoxypropane (Methylpropyl ether), 1-methoxy-2-methylpropane (Methyl 2-methylpropyl ether)
+Os-Cp-Cg-Oh   1         0.40             0.0            2.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Os DiEthers
+H1-Cp-Cg-Cp   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+H1-Cp-Cp-Cg   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+H1-Cg-Cp-Cp   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+H1-Cp-Cp-Cp   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+Cp-Cg-Cp-Cp   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cp-Cg-Cg-Cp   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cg-Cp-Cp-Cg   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cp-Cp-Cg-Cg   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cg-Cp-Cg-Cp   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cg-Cp-Cp-Cp   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cp-Cg-Cp-Cg   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Cp-Cp-Cp-Cg   1         0.45             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Cg-Cg-Cg-Cg Butane
+Os-Cp-Cg-Cp   1        -0.27             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Cg 1-methoxypropane (Methylpropyl ether), 1-methoxy-2-methylpropane (Methyl 2-methylpropyl ether)
+Ho-Oh-Cg-Cp   1         0.18             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Ho-Oh-Cg-Cp Ethanol, propan-2-ol (Isopropanol)
+Oh-Cg-Cp-H1   1         0.05             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Oh-Cg-Cg-H1 tert-butanol
+Os-Cp-Cp-Cg   1        -0.27             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Cg 1-methoxypropane (Methylpropyl ether), 1-methoxy-2-methylpropane (Methyl 2-methylpropyl ether)
+Os-Cp-Cp-Cp   1        -0.27             0.0            1.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Cg 1-methoxypropane (Methylpropyl ether), 1-methoxy-2-methylpropane (Methyl 2-methylpropyl ether)
+P -Os-Cp-Cp   1         0.10             0.0           -3       SCEE=1.0 SCNB=1.0     GLYCAM06j // P -Os-Cp-Cg Methyl ethyl phosphate
+              1         0.05             0.0           -2       SCEE=1.0 SCNB=1.0
+              1        -1.20             0.0            1       SCEE=1.0 SCNB=1.0
+oH-P -Os-Cp   1         0.10             0.0           -3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // O2-P -Os-Cp Dimethyl phosphate
+              1        -0.50             0.0           -2.      SCEE=1.0 SCNB=1.0
+              1         0.10             0.0            1       SCEE=1.0 SCNB=1.0
+H1-Cp-Cp-H1   1         0.17             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-H1 Ethanol
+H1-Cp-Cp-Os   1         0.05             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Os Methoxyethane
+Oh-Cg-Cp-Cp   1         0.10             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Oh-Cg-Cg-Cg 2,3-Dimethylbutanol
+H1-Cg-Cp-Cp   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+H1-Cp-Cp-Cg   1         0.15             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // H1-Cg-Cg-Cg 2,2-Dimethylbutanol
+Oh-Cg-Cp-Cg   1         0.10             0.0            3.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Oh-Cg-Cg-Cg 2,3-Dimethylbutanol
+Os-Cp-Cp-Os   1         0.40             0.0            2.      SCEE=1.0 SCNB=1.0     GLYCAM06j // Os-Cg-Cg-Os DiEthers
+hO-oH-P -Os   3         0.7500           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // hO-oH-pA-oT Lipid17 v1.1  (parm99 X -OH-P -X )
+hO-oH-P -O2   3         0.7500           0.00           3.00    SCEE=1.2 SCNB=2.0     lipid17 // hO-oH-pA-oT Lipid17 v1.1  (parm99 X -OH-P -X )
+
+
+
+IMPROPER
+
+NONB
+  cE          1.8606  0.0988
+
+END

packmol_memgen/data/frcmod.solvents

@@ -0,0 +1,129 @@
+Solvents frcmod file // Mix with AMBER protein FF
+MASS
+SD  32.060        DMSO S
+SK  12.01         DMSO C
+SI  1.008         DMSO H
+S0  16.00         DMSO O
+YK  12.01         Acetonitrile sp C
+YN  14.01         Acetonitrile sp N
+TF  19.00         Trifluoroethanol F
+TO  16.00         Trifluoroethanol O
+TC  12.01         Trifluoroethanol C
+PC  12.01         C sp3 OPLS
+PK  12.01         C sp2 ketone OPLS
+PH  1.008         H OPLS
+PA  12.01         C arom. OPLS
+PI  1.008         H arom. OPLS
+PB  12.01         C arom. OH phenol OPLS
+PO  12.01         O phenol OPLS
+PJ  1.008         H -OH phenol OPLS
+MO  16.00         NMA frcmod
+
+BOND
+SK-SD  240.000   1.800                      STRADER 10.1021/jp013658n
+SD-S0  540.000   1.530                      STRADER 10.1021/jp013658n
+SK-SI  322.000   1.110                      STRADER 10.1021/jp013658n 
+CT-YK  400.000   1.458                      PARM CT-CY
+YK-YN  600.000   1.157                      NIKITIN 10.1002/jcc.20721
+TC-TF  363.800   1.344                      VYMETAL 10.1021/jp505861b
+TC-TC  303.100   1.535                      VYMETAL 10.1021/jp505861b
+TC-TO  314.100   1.426                      VYMETAL 10.1021/jp505861b
+TC-H1  335.900   1.093                      VYMETAL 10.1021/jp505861b
+TO-HO  369.600   0.974                      VYMETAL 10.1021/jp505861b
+PC-PK  317.000   1.522                      PARM CT-C
+PK-O   570.000   1.229                      PARM C -O
+PC-PH  340.000   1.090                      PARM CT-HC
+PA-PA  469.000   1.400                      PARM CA-CA
+PA-PI  367.000   1.080                      PARM CA-HA
+PO-PJ  553.000   0.960                      PARM OH-HO
+PB-PO  450.000   1.364                      PARM C -OH
+PB-PA  469.000   1.409                      PARM C -CA
+C -MO  570.000   1.229                      PARM C -O
+
+ANGL
+SK-SD-S0    79.000  106.750                 STRADER 10.1021/jp013658n
+SK-SD-SK    34.000  95.000                  STRADER 10.1021/jp013658n
+SI-SK-SD    46.100  111.300                 STRADER 10.1021/jp013658n
+SI-SK-SI    35.500  108.400                 STRADER 10.1021/jp013658n
+HC-CT-YK    35.000  110.000                 NIKITIN 10.1002/jcc.20721
+CT-YK-YN    80.000  180.000                 NIKITIN 10.1002/jcc.20721
+TC-TC-TO    67.700  109.430                 VYMETAL 10.1021/jp505861b
+TF-TC-TF    71.300  107.160                 VYMETAL 10.1021/jp505861b
+TF-TC-TC    66.200  109.410                 VYMETAL 10.1021/jp505861b
+TC-TC-H1    46.400  110.070                 VYMETAL 10.1021/jp505861b
+TC-TO-HO    47.100  108.160                 VYMETAL 10.1021/jp505861b
+H1-TC-H1    39.200  109.550                 VYMETAL 10.1021/jp505861b
+H1-TC-TO    51.000  109.880                 VYMETAL 10.1021/jp505861b
+PC-PK-O     80.000  120.400                 PARM CT-C -O                   
+PC-PK-PC    63.000  117.000                 PARM CT-C -CT
+PH-PC-PH    35.000  109.500                 PARM HC-CT-HC
+PH-PC-PK    50.000  109.500                 PARM HC-CT-C
+PA-PA-PA    63.000  120.000                 PARM CA-CA-CA
+PA-PA-PI    50.000  120.000                 PARM CA-CA-HA
+PB-PA-PA    63.000  120.000                 PARM C -CA-CA   
+PO-PB-PA    70.000  120.000                 PARM OH-C -CA
+PA-PB-PA    63.000  120.000                 PARM CA-C -CA
+PB-PO-PJ    50.000  113.000                 PARM C -OH-HO
+PB-PA-PI    50.000  120.000                 PARM C -CA-HA
+CT-C -MO    80.000  120.400                 PARM CT-C -O
+MO-C -N     80.000  122.900                 PARM O -C -N
+
+DIHE
+SK-SD-SK-SI    1     0.20000000    0.000   3.0    SCEE=1.2 SCNB=2.0 STRADER 10.1021/jp013658n
+SI-SK-SD-S0    1     0.20000000    0.000   3.0    SCEE=1.2 SCNB=2.0 STRADER 10.1021/jp013658n
+HC-CT-YK-YN    1     0.00000000    0.000   1.0    SCEE=1.2 SCNB=2.0 PARM  HC-CT-CY-NY
+TF-TC-TC-TO    1     0.15600000    0.000   3.0    SCEE=1.2 SCNB=2.0 PARM F -CT-CT-OH
+TC-TC-TO-HO    1     0.42900000    0.000  -1.0    SCEE=1.2 SCNB=2.0 VYMETAL 10.1021/jp505861b
+TC-TC-TO-HO    1     0.16000000    0.000   3.0    SCEE=1.2 SCNB=2.0 PARM CT-CT-OH-HO
+TF-TC-TC-H1    1     0.19000000    0.000  -1.0    SCEE=1.2 SCNB=2.0 PARM F -CT-CT-H1
+TF-TC-TC-H1    1     0.15600000    0.000   3.0    SCEE=1.2 SCNB=2.0 VYMETAL 10.1021/jp505861b
+H1-TC-TO-HO    1     0.16700000    0.000   3.0    SCEE=1.2 SCNB=2.0 PARM H1-CT-OH-HO
+PC-PK-PC-PH    1     0.00000000    0.000   2.0    SCEE=1.2 SCNB=2.0 PARM CT-C -CT-HC
+PH-PC-PK-O     1     0.80000000    0.000  -1.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O  
+PH-PC-PK-O     1     0.00000000    0.000  -2.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O
+PH-PC-PK-O     1     0.08000000  180.000   3.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O
+PA-PA-PA-PA    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM CA-CA-CA-CA
+PA-PA-PA-PI    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM CA-CA-CA-HA
+PI-PA-PA-PI    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM HA-CA-CA-HA
+PB-PA-PA-PA    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM C -CA-CA-CA
+PO-PB-PA-PA    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM OH-C -CA-CA
+PA-PB-PA-PA    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM CA-C -CA-CA
+PB-PA-PA-PI    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM C -CA-CA-HA
+PO-PB-PA-PI    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM OH-C -CA-HA
+PA-PB-PO-PJ    1     0.00000000    0.000  -1.0    SCEE=1.2 SCNB=2.0 PARM CA-C -OH-HO
+PA-PB-PO-PJ    1     0.88300000  180.000  -2.0    SCEE=1.2 SCNB=2.0 PARM CA-C -OH-HO
+PA-PB-PO-PJ    1     0.00000000    0.000  -3.0    SCEE=1.2 SCNB=2.0 PARM CA-C -OH-HO
+PA-PB-PO-PJ    1     0.06500000    0.000   4.0    SCEE=1.2 SCNB=2.0 PARM CA-C -OH-HO
+PA-PB-PA-PI    1     3.62500000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM CA-C -CA-HA
+MO-C -N -CT    1     2.50000000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM O -C -N -CT
+HC-CT-C -MO    1     0.80000000    0.000  -1.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O 
+HC-CT-C -MO    1     0.00000000    0.000  -2.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O 
+HC-CT-C -MO    1     0.08000000  180.000   3.0    SCEE=1.2 SCNB=2.0 PARM HC-CT-C -O 
+MO-C -N -H     1     2.00000000    0.000  -1.0    SCEE=1.2 SCNB=2.0 PARM O -C -N -H 
+MO-C -N -H     1     2.50000000  180.000   2.0    SCEE=1.2 SCNB=2.0 PARM O -C -N -H 
+
+IMPROPER
+PA-PA-PA-PI     1.10000000  180.000   2.0   PARM CA-CA-CA-HA
+PA-PA-PB-PO     1.10000000  180.000   2.0   PARM CA-CA-C -OH
+PB-PA-PA-PI     1.10000000  180.000   2.0   PARM C -CA-CA-HA
+CT-N -C -MO    10.50000000  180.000   2.0   PARM CT-N -C -O
+
+NONB
+SD    2.00000000   0.35000000               STRADER 10.1021/jp013658n
+SK    2.04000000   0.07800000               STRADER 10.1021/jp013658n
+SI    1.34000000   0.02400000               STRADER 10.1021/jp013658n
+S0    1.70000000   0.12000000               STRADER 10.1021/jp013658n
+YN    1.69000000   0.13310000               NIKITIN 10.1002/jcc.20721
+YK    1.99000000   0.13410000               NIKITIN 10.1002/jcc.20721
+TF    1.81376397   0.00818924               VYMETAL 10.1021/jp505861b
+TC    1.90800360   0.10940000               VYMETAL 10.1021/jp505861b PARM CT
+TO    1.72100000   0.21040000               PARM OH
+PC    1.96430000   0.06600000               C sp3 OPLS
+PK    2.10460000   0.10500000               C sp2 ketone OPLS
+PH    1.35820000   0.01500000               H - C sp3 OPLS
+PA    1.99240000   0.07000000               C arom. OPLS
+PI    1.35820000   0.03000000               H arom. OPLS
+PO    1.72300000   0.17000000               OH phenol OPLS
+PJ    0.00000000   0.00000000               H OH phenol OPLS
+PB    1.99240000   0.07000000               C - OH phenol OPLS
+MO    1.76830000   0.15200000               NMA frcmod

packmol_memgen/data/insane_lipids.txt

@@ -0,0 +1,138 @@
+# Generated from Insane4MemPrO
+# Source: /home/youmans/work/SPONGE_toolkits/membrane_builder/packmol_memgen_minimal/.venv/lib/python3.13/site-packages/mempro/Insane4MemPrO.py
+# Count: 134
+AMA
+AMA.w
+APG
+BFRA
+BNSM
+BPER
+CARD
+CDL0
+CDL1
+CDL2
+CER.o
+CHOL
+CJEJ
+CL4.o
+CL4M
+CL4O.o
+CL4P
+CPG.o
+CTRA
+CYSD
+CYST
+DAPC
+DBPC
+DBPE
+DBSM
+DEPC.o
+DFGG
+DFMG
+DGDG.o
+DGPC
+DHPC.o
+DHPE.o
+DIPC
+DLPC
+DLPE
+DLPE.o
+DMPC.o
+DMPE.o
+DNPC
+DOPC
+DOPC.o
+DOPE
+DOPE.o
+DOPG
+DOPG.o
+DOPS
+DOPS.o
+DPCE
+DPG1
+DPG3
+DPGG
+DPGS
+DPMG
+DPPC
+DPPE
+DPPI
+DPPI.o
+DPSG
+DPSM
+DSDG.o
+DSMG.o
+DSPC.o
+DSPE.o
+DSSQ.o
+DTPC
+DTPE
+DUPC.o
+DXG1
+DXG3
+ERGO
+FPGG
+FPMG
+FPSG
+GCER.o
+GM1.o
+GMO
+HBHT
+HDPT
+HHOP
+HOPR
+HPYL
+JFPG
+JPPG
+KMA
+KLA
+KPG
+LI10
+LI12
+LI14
+LI16
+LI18
+LI20
+LI22
+LIP2
+LIP4
+LIP6
+LIP8
+MGDG.o
+MMA
+NAM
+NMEN
+OPGG
+OPMG
+OPPG
+OPSG
+PAPI
+PGIN
+PI.o
+PI34.o
+PIPI
+PLQ
+PNG1
+PNG3
+POP1
+POP2
+POP3
+POPC
+POPC.o
+POPE
+POPE.o
+POPG
+POPG.o
+POPI
+POPS
+POPS.o
+PPCS.o
+PPG.o
+PPT.o
+PUPI
+SMIN
+SPEP
+SQDG.o
+UUPEP
+XNG1
+XNG3

packmol_memgen/data/insane_solvents.txt

@@ -0,0 +1,45 @@
+# Generated from Insane4MemPrO
+# Source: /home/youmans/work/SPONGE_toolkits/membrane_builder/packmol_memgen_minimal/.venv/lib/python3.13/site-packages/mempro/Insane4MemPrO.py
+# Count: 42
+ALA
+ARG
+ASN
+ASP
+BMW
+BUT
+CELL
+CL
+CYS
+FG4W
+FG4W-MS
+FRUC
+GLN
+GLU
+GLUC
+GLY
+HYP
+ILE
+K
+KOJI
+LAMI
+LEU
+LYS
+MALT
+MET
+Mg
+NA
+NIGE
+PHE
+PRO
+PW
+SER
+SOPH
+SPC
+SPCM
+SUCR
+THR
+TREH
+TRP
+TYR
+VAL
+W

packmol_memgen/data/leaprc.extra_solvents

@@ -0,0 +1,42 @@
+#
+# Set log file
+#
+logFile leap.log
+#
+# leaprc for loading extra solvents
+# Parameters from:
+#   STRADER 10.1021/jp013658n
+#   NIKITIN 10.1002/jcc.20721
+#   VYMETAL 10.1021/jp505861b
+#   
+# Load atom type hybridizations
+#
+addAtomTypes {
+    { "SD"  "S" "sp3" }
+    { "SK"  "C" "sp3" }
+    { "SI"  "H" "sp3" }
+    { "S0"  "O" "sp3" }
+    { "YK"  "C" "sp" }
+    { "YN"  "N" "sp" }
+    { "TF"  "F" "sp3" }
+    { "TO"  "O" "sp3" }
+    { "TC"  "C" "sp3" }
+    { "PC"  "C" "sp3" }
+    { "PK"  "C" "sp2" }
+    { "PH"  "H" "sp3" }
+    { "PA"  "C" "sp2" }
+    { "PI"  "H" "sp3" }
+    { "PB"  "C" "sp2" }
+    { "PO"  "O" "sp3" }
+    { "PJ"  "H" "sp3" }
+    { "MO"  "O" "sp2" }
+}
+#
+# Load the Lipid17 parameter set.
+#
+extra_solvents = loadamberparams frcmod.solvents
+chloroform     = loadamberparams frcmod.chcl3
+#
+# Load the Lipid17 master lib file.
+#
+loadoff extra_solvents.lib

packmol_memgen/data/leaprc.lipid_ext

@@ -0,0 +1,48 @@
+#
+# Set log file
+#
+logFile leap.log
+#
+# leaprc for loading the Lipid17 extended force field
+#       
+# Load atom type hybridizations
+#
+addAtomTypes {
+    { "cE"  "C" "sp2" }
+    { "C"   "C" "sp2" }
+    { "Cg"  "C" "sp3" }
+    { "Cy"  "C" "sp3" }
+    { "Ck"  "C" "sp2" }
+    { "CT"  "C" "sp3" }
+    { "Cj"  "C" "sp2" }
+    { "Cp"  "C" "sp3" }
+    { "H"   "H" "sp3" }
+    { "H1"  "H" "sp3" }
+    { "H2"  "H" "sp3" }
+    { "Ha"  "H" "sp3" }
+    { "Hp"  "H" "sp3" }
+    { "Hc"  "H" "sp3" }
+    { "Ho"  "H" "sp3" }
+    { "HW"  "H" "sp3" }
+    { "Ng"  "N" "sp2" }
+    { "NT"  "N" "sp3" }
+    { "N3"  "N" "sp3" }
+    { "Oh"  "O" "sp3" }
+    { "Os"  "O" "sp3" }
+    { "O"   "O" "sp2" }
+    { "O2"  "O" "sp2" }
+    { "OW"  "O" "sp3" }
+    { "Oy"  "O" "sp3" }
+    { "S"   "S" "sp3" }
+    { "Sm"  "S" "sp3" }
+    { "P"   "P" "sp3" }
+}
+#
+# Load the Lipid17 parameter set.
+#
+glycam_06 = loadamberparams GLYCAM_06j.dat
+lipid_ext = loadamberparams frcmod.lipid_ext
+#
+# Load the Lipid17 master lib file.
+#
+loadoff lipid_ext.lib