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addition of CH1t THR good setup IDP LLPS #615

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Merged
carlocamilloni merged 4 commits into from
Mar 11, 2026
Merged

addition of CH1t THR good setup IDP LLPS #615

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decd4a9
fixed output bug for cross cmdata output in h5
brunostega Mar 7, 2026
7fa830b
Merge remote-tracking branch 'refs/remotes/origin/new_dih' into new_dih
brunostega Mar 9, 2026
f7385f8
minor modification of OM reps and other adjustments for LLPS
brunostega Mar 10, 2026
fe80963
addition of CH1t and code refinment
brunostega Mar 11, 2026
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2 changes: 1 addition & 1 deletion multi-ego-basic.ff/aminoacids.rtp
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Original file line number Diff line number Diff line change
Expand Up @@ -934,7 +934,7 @@
N N 0.000 0
H H 0.000 0
CA CAH 0.000 0
CB CH1 0.000 0
CB CH1t 0.000 0
OG1 OA 0.000 0
CG2 CH3 0.000 0
C C 0.000 0
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1 change: 1 addition & 0 deletions multi-ego-basic.ff/atomtypes.atp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
CH 13.01900 ; aromatic CH
CAH 12.01100 ; aliphatic or sugar CH-group
CH1 13.01900 ; aliphatic or sugar CH-group
CH1t 13.01900 ; aliphatic or sugar CH-group
CH2 14.02700 ; aliphatic or sugar CH2-group
CAH2 14.02700 ; aliphatic or sugar CH2-group
CH3 15.03500 ; aliphatic CH3-group
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1 change: 1 addition & 0 deletions multi-ego-basic.ff/ffnonbonded.itp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
H 1 0.000 0.000 A 0.0000000000 3.239247e-09
CAH 6 0.000 0.000 A 0.0000000000 6.555574e-05
CH1 6 0.000 0.000 A 0.0000000000 6.555574e-05
CH1t 6 0.000 0.000 A 0.0000000000 6.555574e-05
CH2 6 0.000 0.000 A 0.0000000000 1.543890e-05
CAH2 6 0.000 0.000 A 0.0000000000 1.543890e-05
CH3 6 0.000 0.000 A 0.0000000000 8.595562e-06
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63 changes: 49 additions & 14 deletions src/multiego/resources/type_definitions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,13 @@
import sys

mg_OO_c12_rep = 7.5e-7
mg_OMOM_c12_rep = 2.5e-5
mg_OMOM_c12_rep = 2.5e-6 # This might be shifted down looking at ATDhisto
mg_HH_c12_rep = 1.2e-8
mg_ON_c12_rep = 7.5e-7
mg_NN_c12_rep = 2.5e-5

mg_HO_sigma = 0.169500
mg_eps_HO = 0.17
mg_eps_HO = 0.15

eps_O = 0.085
eps_OM = 0.085
Expand All @@ -23,7 +23,8 @@
eps_C = 0.085
eps_CZ = 0.085
eps_CH = 0.15
eps_CH1 = 0.085
eps_CH1 = 0.010
eps_CH1t = 0.085
eps_CAH = 0.085
eps_CH2 = 0.13
eps_CAH2 = 0.15
Expand Down Expand Up @@ -55,6 +56,7 @@
"CZ",
"CH",
"CH1",
"CH1t",
"CAH",
"CH2",
"CAH2",
Expand All @@ -69,7 +71,7 @@
"H",
"C0",
],
"at.num": [8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 6, 15, 8, 6, 1, 20],
"at.num": [8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 6, 15, 8, 6, 1, 20],
"rc_c12": [
2.5 * 0.262134**12, # "O", 2.631580e-07
2.5 * 0.253061**12, # "OM", 1.724403e-07
Expand All @@ -84,6 +86,7 @@
2.5 * 0.317248**12, # "CZ", 2.598570e-06
2.5 * 0.317248**12, # "CH", 2.598570e-06
2.5 * 0.415167**12, # "CH1", 6.555574e-05
2.5 * 0.415167**12, # "CH1t", 6.555574e-05
2.5 * 0.415167**12, # "CAH", 6.555574e-05
2.5 * 0.368035**12, # "CH2", 1.543890e-05
2.5 * 0.368035**12, # "CAH2",1.543890e-05
Expand Down Expand Up @@ -113,6 +116,7 @@
4.0 * 0.35812**12 * eps_CZ, # "CZ", sig=0.35812
4.0 * 0.35812**12 * eps_CH, # "CH", sig=0.35812
4.0 * 0.44592**12 * eps_CH1, # "CH1", sig=0.50192
4.0 * 0.44592**12 * eps_CH1t, # "CH1t", sig=0.50192
4.0 * 0.44592**12 * eps_CAH, # "CAH", sig=0.50192
4.0 * 0.40704**12 * eps_CH2, # "CH2", sig=0.40704
4.0 * 0.40704**12 * eps_CAH2, # "CAH2", sig=0.40704
Expand Down Expand Up @@ -141,6 +145,7 @@
4.0 * 0.35812**6 * eps_CZ, # "C",
4.0 * 0.35812**6 * eps_CH, # "CH"
4.0 * 0.44592**6 * eps_CH1, # "CH1"
4.0 * 0.44592**6 * eps_CH1t, # "CH1t"
4.0 * 0.44592**6 * eps_CAH, # "CAH"
4.0 * 0.40704**6 * eps_CH2, # "CH2"
4.0 * 0.40704**6 * eps_CAH2, # "CAH2"
Expand Down Expand Up @@ -260,7 +265,7 @@ def lj14_generator(df):
{
"atomtypes": (
["NZ"],
["N", "NT", "NR", "C", "CH1", "CAH", "CH2", "CAH2", "CH3"],
["N", "NT", "NR", "C", "CH1", "CAH", "CH2", "CH3"],
), # Repulsion of charged N with all but CH, CH2r (aromatic) and CZ, NE (for ARG-ARG interactions)
"interaction": "rep",
"sigma": None,
Expand All @@ -269,29 +274,44 @@ def lj14_generator(df):
{
"atomtypes": (
["NL"],
["N", "NT", "NR", "C", "NE", "CZ", "CH1", "CAH", "CH2", "CAH2", "CH3", "CH2r"],
["N", "NT", "NR", "C", "NE", "CZ", "CH1", "CAH", "CH2", "CH3", "CH2r"],
), # Repulsion of charged N with all but CH (interacts less then NZ to make ARG stickier than LYS)
"interaction": "rep",
"sigma": None,
"epsilon": None,
},
{
"atomtypes": (
["OM"],
["CH", "CH1", "CAH", "CH2", "CAH2", "CH3", "CH2r", "S"],
), # repulsion of charged O with hydrophobic
["NL", "NZ"],
["CAH2", "CH1t"],
), # Weak interaction of charged N based on hyd of CAH2 from local fingerprint Parrinello and ATDhisto contact probability
"interaction": "att",
"sigma": None,
"epsilon": 0.085,
},
{
"atomtypes": (["OM"], ["CH", "CH1", "CAH", "CH3", "CH2r", "S"]), # repulsion of charged O with hydrophobic
"interaction": "rep",
"sigma": None,
"epsilon": None,
},
{
"atomtypes": (["NZ", "CZ", "NE"], ["CH"]), # catyon-pi generic
"atomtypes": (
["OM"],
["CAH2", "CH2", "CH1t"],
), # Weak interaction of OM based on hyd of CAH2 and CH2 (Not sure about CH2) from local fingerprint Parrinello and ATDhisto contact probability
"interaction": "att",
"sigma": None,
"epsilon": 0.085,
},
{
"atomtypes": (["NZ", "CZ", "NE"], ["CH"]), # cation-pi generic
"interaction": "att",
"sigma": None,
"epsilon": 0.13,
},
{
"atomtypes": (["NL"], ["CH"]), # catyon-pi generic
"atomtypes": (["NL"], ["CH"]), # cation-pi generic
"interaction": "att",
"sigma": None,
"epsilon": 0.10,
Expand All @@ -315,17 +335,32 @@ def lj14_generator(df):
"epsilon": 0.07,
},
{
"atomtypes": (["OA", "SH"], ["CH"]), # weaker OA-CH and SH-CH catyon-pi interaction
"atomtypes": (["OA", "SH"], ["CH"]), # weaker OA-CH and SH-CH cation-pi interaction
"interaction": "att",
"sigma": None,
"epsilon": 0.11,
"epsilon": 0.10,
},
{
"atomtypes": (["OA"], ["NR", "NT", "NE", "S", "O", "OA", "OM", "NZ", "NL"]), # H-bond of OA with polar and charged
"atomtypes": (
["OA"],
["NR", "NT", "NE", "S", "O", "OA", "OM", "NZ", "NL", "CH1t"],
), # H-bond of OA with polar and charged
"interaction": "att",
"sigma": None,
"epsilon": mg_eps_HO,
},
{
"atomtypes": (["OA"], ["CH2", "CH3", "CAH2"]), # H-bond of OA with polar and charged
"interaction": "att",
"sigma": None,
"epsilon": 0.085,
},
{
"atomtypes": (["CH1t"], ["CH2", "CH3", "CAH2", "CH1", "CH"]), # H-bond of OA with polar and charged
"interaction": "att",
"sigma": None,
"epsilon": 0.085,
},
{
"atomtypes": (["OM"], ["NL", "NZ", "NE"]), # salt bridges
"interaction": "att",
Expand Down
8 changes: 4 additions & 4 deletions tools/cmdata/src/cmdata/io.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -325,22 +325,22 @@ void f_write_inter_cross_HDF5(const std::string &output_prefix,
const std::vector<std::vector<std::vector<std::vector<float>>>> &interm_cross_maxcdf_mol
)
{
std::string file_name = output_prefix + "inter_mol_" + std::to_string(i + 1) + "_" + std::to_string(i + 1) + "_aa_" + std::to_string(ii + 1) + ".h5";
std::string file_name_c = output_prefix + "inter_mol_c_" + std::to_string(i + 1) + "_" + std::to_string(i + 1) + "_aa_" + std::to_string(ii + 1) + ".h5";
std::string file_name = output_prefix + "inter_mol_" + std::to_string(i + 1) + "_" + std::to_string(j + 1) + "_aa_" + std::to_string(ii + 1) + ".h5";
std::string file_name_c = output_prefix + "inter_mol_c_" + std::to_string(i + 1) + "_" + std::to_string(j + 1) + "_aa_" + std::to_string(ii + 1) + ".h5";
// Create a new HDF5 file using the default settings.
H5File file(file_name.c_str(), H5F_ACC_TRUNC);
H5File file_c(file_name_c.c_str(), H5F_ACC_TRUNC);

// Define the dimensions of the dataset
hsize_t dims[2] = {static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(natmol2[i]+1)};
hsize_t dims[2] = {static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(natmol2[j]+1)};
DataSpace dataspace(2, dims);

// Create dataset creation property list with compression
DSetCreatPropList plist;
plist.setDeflate(6); // Set compression level (0-9, where 9 is maximum compression)
hsize_t chunk_dims[2] = {
std::min(static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(300)),
std::min(static_cast<hsize_t>(natmol2[i] + 1), static_cast<hsize_t>(512))
std::min(static_cast<hsize_t>(natmol2[j] + 1), static_cast<hsize_t>(512))
};
plist.setChunk(2, chunk_dims);

Expand Down
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