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Corrected serious mistakes in the improper interactions defined in th…
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…e oplsaa.lt file (2023 version). (I verified the new version of oplsaa.lt is correct by confirming that the number and magnitude of the impropers generated by moltemplate (for ethylene and benzioc-acid) agree with impropers generated by the ligpargen server for these molecules.) I am now confident that the improper interactions in the latest oplsaa.lt file are correct! (There is one exception: allenes. The original BOSS filse have non-sensical improper interactions for allenes. So the oplsaa2lt.py conversion script comments those out.) The conversion script (oplsaa2lt.py) is also working, so there is no longer a need to hand-edit the generated oplsaa.lt file afterwards. Please update your oplsaa.lt files to this version. Previous versions will not work.
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@jewettaij
jewettaij committed Dec 4, 2024
1 parent e10f1f2 commit e56e240
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30 changes: 25 additions & 5 deletions moltemplate/force_fields/convert_OPLSAA_to_LT/oplsaa2lt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,12 @@ def rename_type(ty: str) -> str:
ty = ty.strip()
for orig, changed in TYPE_CONVERSION_TUPLES:
ty = ty.replace(orig, changed)
if ty in ["X", "Y", "Z"]:
# In BOSS files, "X", "Y", "Z" indicate wildcards
ty = "??" # But here we use "??" to indicate wildcards
if len(ty) == 1:
# It is a good idea to make sure these strings are the same length (2).
ty += '~' # (eg "C"->"C~") It doesn't matter which character we add
ty += "~" # (eg "C"->"C~") It doesn't matter which character we add
assert len(ty) == 2 # The "ty" strings should all be 2-characters long.
return ty

Expand Down Expand Up @@ -131,11 +134,28 @@ def get_dihedrals_and_impropers(input_lines) -> tuple[list[Dihedral], list[Impro
if dihed_definition.endswith("P in"):
dihed_definition = dihed_definition.replace("P in", "P")
types = list(map(rename_type, dihed_definition.split('-')))
assert len(types) == 4
comment = l[DEFINITION_END+1:].strip()
#if dihed_definition == "HC-CT-CT-C(O)"
if "improper" in comment:
loaded_impropers.append(
Improper(types=types, v1=v1, v2=v2, v3=v3, v4=v4, comment=comment))
# I've had good results using the "cenIsortJKL.py" symmetry
# rules with OPLSAA. (When I use those settings, the resulting
# LAMMPS data files agrees with the data files from LigParGen.)
# But in order for this to work, we need to swap the first two atom
# types, since now the first atom is the center. -Andrew 2024-12-04
types = [types[1], types[0], types[2], types[3]] # see above comment
improper = Improper(types=types, v1=v1, v2=v2, v3=v3, v4=v4, comment=comment)
# There is a weird problem with "allenes improper" interactions
# that appear in the 2023 version of the BOSS files.
# Those files specify improper interactions between atoms
# that are typically collinear. That would be numerically
# unstable so we must comment these out. This seems like
# a bug in the BOSS files. Perhaps later I'll report this.
# But for now, I just comment them out.
if comment.strip() == "allenes improper":
improper.to_comment = True

loaded_impropers.append(improper)

else:
loaded_dihedrals.append(
Dihedral(types=types, v1=v1, v2=v2, v3=v3, v4=v4, comment=comment))
Expand Down Expand Up @@ -404,7 +424,7 @@ def main(argv):
if not improper.to_skip:
outfile.write(f" {improper.coeff_line}")
outfile.write(" } # (end of improper_coeffs)\n")
outfile.write('\n write_once("Data Impropers By Type (opls_imp.py)") {\n')
outfile.write('\n write_once("Data Impropers By Type (cenIsortJKL.py)") {\n')
for improper in impropers:
if not improper.to_skip:
outfile.write(f" {improper.bytype_line}")
Expand Down
38 changes: 23 additions & 15 deletions moltemplate/force_fields/convert_OPLSAA_to_LT/oplsaa2lt_classes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,7 @@ def __init__(self, types: list[str], comment: str):
self.comment = comment
self.duplicate_count = 0
self.to_skip = False
self.to_comment = False

@property
def ty1(self) -> str:
Expand Down Expand Up @@ -190,6 +191,12 @@ def _duplicate_count_str(self) -> str:
return f"__{self.duplicate_count}"
return ""

@property
def _prepend_comment_if_needed(self) -> str:
if self.to_comment:
return "# UNTRUSTED: "
return ""


class Bond(BondedInteraction):
kind = "bond"
Expand All @@ -203,15 +210,17 @@ def __init__(self, types: list[str], k: str, eq: str, comment: str):

@property
def bytype_line(self) -> str:
l = f"@{type(self).kind}:{self.typename}"
l = self._prepend_comment_if_needed
l += f"@{type(self).kind}:{self.typename}"
l += f"{self._duplicate_count_str}"
l += f" @atom:*_b{self.ty1}*_a*_d*_i*"
l += f" @atom:*_b{self.ty2}*_a*_d*_i*\n"
return l

@property
def coeff_line(self) -> str:
l = f"{self._coeff_line_base}{self._duplicate_count_str} {self.k} {self.eq} # {self.comment}\n"
l = self._prepend_comment_if_needed
l += f"{self._coeff_line_base}{self._duplicate_count_str} {self.k} {self.eq} # {self.comment}\n"
return l


Expand All @@ -227,7 +236,8 @@ def __init__(self, types: list[str], k: str, eq: str, comment: str):

@property
def bytype_line(self) -> str:
l = f"@{type(self).kind}:{self.typename}"
l = self._prepend_comment_if_needed
l += f"@{type(self).kind}:{self.typename}"
l += f"{self._duplicate_count_str}"
l += f" @atom:*_b*_a{self.ty1}*_d*_i*"
l += f" @atom:*_b*_a{self.ty2}*_d*_i*"
Expand All @@ -236,7 +246,8 @@ def bytype_line(self) -> str:

@property
def coeff_line(self) -> str:
l = f"{self._coeff_line_base}{self._duplicate_count_str} {self.k} {self.eq} # {self.comment}\n"
l = self._prepend_comment_if_needed
l += f"{self._coeff_line_base}{self._duplicate_count_str} {self.k} {self.eq} # {self.comment}\n"
return l


Expand All @@ -251,7 +262,8 @@ def __init__(self, types: list[str], v1, v2, v3, v4, comment: str):

@property
def bytype_line(self) -> str:
l = f"@{type(self).kind}:{self.typename}"
l = self._prepend_comment_if_needed
l += f"@{type(self).kind}:{self.typename}"
l += f"{self._duplicate_count_str}"
l += f" @atom:*_b*_a*_d{self.ty1}*_i*"
l += f" @atom:*_b*_a*_d{self.ty2}*_i*"
Expand All @@ -261,7 +273,8 @@ def bytype_line(self) -> str:

@property
def coeff_line(self) -> str:
l = f"{self._coeff_line_base}{self._duplicate_count_str} {self.v1} {self.v2} {self.v3} {self.v4}"
l = self._prepend_comment_if_needed
l += f"{self._coeff_line_base}{self._duplicate_count_str} {self.v1} {self.v2} {self.v3} {self.v4}"
l += f" # {self.comment} \n"
return l

Expand All @@ -275,16 +288,10 @@ def __init__(self, types: list[str], v1, v2, v3, v4, comment: str):
self.v1, self.v2, self.v3, self.v4 = v1, v2, v3, v4
self.comment = comment

# replacing every X/Y/Z with "*", I don't know if that's the correct approach,
# as if this was the intended behaviour I think in the FF file they would have used
# "*", as they did in the dihedrals sections...
for i, ty in enumerate(self.types):
if ty in ("X", "Y", "Z"):
self.types[i] = "*"

@property
def bytype_line(self) -> str:
l = f"@{type(self).kind}:{self.typename}"
l = self._prepend_comment_if_needed
l += f"@{type(self).kind}:{self.typename}"
l += f" @atom:*_b*_a*_d*_i{self.ty1}*"
l += f" @atom:*_b*_a*_d*_i{self.ty2}*"
l += f" @atom:*_b*_a*_d*_i{self.ty3}*"
Expand All @@ -293,8 +300,9 @@ def bytype_line(self) -> str:

@property
def coeff_line(self) -> str:
l = self._prepend_comment_if_needed
# If using "improper_style cvff", then use:
l = f"{self._coeff_line_base}{self._duplicate_count_str} {float(self.v2)/2:.4f} -1 2 # {self.comment}\n"
l += f"{self._coeff_line_base}{self._duplicate_count_str} {float(self.v2)/2:.4f} -1 2 # {self.comment}\n"
# If using "improper_style harmonic", then use this instead:
# l += f"{self._coeff_line_base}{self._duplicate_count_str} {float(self.v2)} 180.0 # {self.comment}\n"
return l
42 changes: 17 additions & 25 deletions moltemplate/force_fields/oplsaa.lt
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Original file line number Diff line number Diff line change
Expand Up @@ -10333,33 +10333,25 @@ OPLSAA {


write_once("In Settings") {
improper_coeff @improper:O~_C~_€€_€€ 10.5000 -1 2 # improper torsion
improper_coeff @improper:€€_CA_€€_€€ 2.5000 -1 2 # improper torsion 9/08 was 2.2
improper_coeff @improper:€€_CM_€€_€€ 15.0000 -1 2 # improper torsion
improper_coeff @improper:€€_N~_€€_€€ 2.5000 -1 2 # improper torsion 9/08 was 2.0
# The next 4 impropers weren't in the 2008 version. They are in the 2023 version
# Unfortunately, they are causing problems, overwriting legitimate impropers.
# For now, I will comment them out.
# Later, I will revisit these -Andrew 2024-12-02
# improper_coeff @improper:CM_CT_CM_CT -4.0000 -1 2 # allenes improper
# improper_coeff @improper:CM_CT_CM_HC -4.0000 -1 2 # allenes improper
# improper_coeff @improper:CM_HC_CM_CT -4.0000 -1 2 # allenes improper
# improper_coeff @improper:CM_HC_CM_HC -4.0000 -1 2 # allenes improper
improper_coeff @improper:CA_€€_€€_€€ 2.5000 -1 2 # improper torsion 9/08 was 2.2
improper_coeff @improper:CM_€€_€€_€€ 15.0000 -1 2 # improper torsion
improper_coeff @improper:N~_€€_€€_€€ 2.5000 -1 2 # improper torsion 9/08 was 2.0
improper_coeff @improper:C~_O~_€€_€€ 10.5000 -1 2 # improper torsion
# UNTRUSTED: improper_coeff @improper:CT_CM_CM_CT -4.0000 -1 2 # allenes improper
# UNTRUSTED: improper_coeff @improper:CT_CM_CM_HC -4.0000 -1 2 # allenes improper
# UNTRUSTED: improper_coeff @improper:HC_CM_CM_CT -4.0000 -1 2 # allenes improper
# UNTRUSTED: improper_coeff @improper:HC_CM_CM_HC -4.0000 -1 2 # allenes improper
} # (end of improper_coeffs)

write_once("Data Impropers By Type (opls_imp.py)") {
@improper:O~_C~_€€_€€ @atom:*_b*_a*_d*_iO~* @atom:*_b*_a*_d*_iC~* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:€€_CA_€€_€€ @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_iCA* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:€€_CM_€€_€€ @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:€€_N~_€€_€€ @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_iN~* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
# The next 4 impropers weren't in the 2008 version. They are in the 2023 version
# Unfortunately, they are causing problems, overwriting legitimate impropers.
# For now, I will comment them out.
# Later, I will revisit these -Andrew 2024-12-02
# @improper:CM_CT_CM_CT @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT*
# @improper:CM_CT_CM_HC @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC*
# @improper:CM_HC_CM_CT @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT*
# @improper:CM_HC_CM_HC @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC*
write_once("Data Impropers By Type (cenIsortJKL.py)") {
@improper:CA_€€_€€_€€ @atom:*_b*_a*_d*_iCA* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:CM_€€_€€_€€ @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:N~_€€_€€_€€ @atom:*_b*_a*_d*_iN~* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
@improper:C~_O~_€€_€€ @atom:*_b*_a*_d*_iC~* @atom:*_b*_a*_d*_iO~* @atom:*_b*_a*_d*_i??* @atom:*_b*_a*_d*_i??*
# UNTRUSTED: @improper:CT_CM_CM_CT @atom:*_b*_a*_d*_iCT* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT*
# UNTRUSTED: @improper:CT_CM_CM_HC @atom:*_b*_a*_d*_iCT* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC*
# UNTRUSTED: @improper:HC_CM_CM_CT @atom:*_b*_a*_d*_iHC* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCT*
# UNTRUSTED: @improper:HC_CM_CM_HC @atom:*_b*_a*_d*_iHC* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iCM* @atom:*_b*_a*_d*_iHC*
} # (end of impropers by type)


Expand Down
2 changes: 1 addition & 1 deletion moltemplate/force_fields/oplsaa2008.lt
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Original file line number Diff line number Diff line change
Expand Up @@ -8207,7 +8207,7 @@ OPLSAA {
# Rules for creating improper interactions according to atom type:
# ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4
# (* = wildcard)
write_once("Data Impropers By Type (opls_imp.py)") {
write_once("Data Impropers By Type (cenKswapIL.py)") {
@improper:X_X_003_004 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i004*
@improper:X_X_003_052 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i052*
@improper:X_X_024_X @atom:* @atom:* @atom:*_b*_a*_d*_i024* @atom:*
Expand Down
0 moltemplate/nbody_alt_symmetry/opls_imp.py → moltemplate/nbody_alt_symmetry/cenKswapIL.py
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