Good afternoon!
I am working on the parameterization of non-standard amino acids and have encountered an issue when generating an ITP file. At some point, one of the nitrogen atoms is assigned the atom type DU, and three protons (hydrogens) bound to it are also given the DU type. However, if I manually provide the PDB to Antechamber, all atom types are correct.
Do you have any ideas what might be causing this?
Here are examples of my code:
molecule = ACTopol(inputFile = f'../molecules/substructure/Lysine_1M_rn_H_3D.pdb',
chargeType="gas", # bcc
atomType='amber',
outTopol='gmx',
basename=full_mol_name,
chargeVal=1,
debug=True
)
molecule.createACTopol()
molecule.createMolTopol()
My pdb:
ATOM 1 N Kme A 2 -3.243 -0.551 0.714 1.00 0.00 N
ATOM 2 CA Kme A 2 -2.781 0.352 -0.342 1.00 0.00 C
ATOM 3 C Kme A 2 -2.598 1.743 0.209 1.00 0.00 C
ATOM 4 O Kme A 2 -2.350 2.675 -0.539 1.00 0.00 O
ATOM 5 CB Kme A 2 -1.478 -0.174 -0.979 1.00 0.00 C
ATOM 6 CG Kme A 2 -0.331 -0.341 0.034 1.00 0.00 C
ATOM 7 CD Kme A 2 0.943 -0.847 -0.659 1.00 0.00 C
ATOM 8 CE Kme A 2 2.059 -1.233 0.334 1.00 0.00 C
ATOM 9 NZ Kme A 2 2.525 -0.121 1.183 1.00 0.00 N1+
ATOM 10 CH Kme A 2 3.154 0.958 0.412 1.00 0.00 C
ATOM 11 HH3 Kme A 2 3.672 1.657 1.104 1.00 0.00 H
ATOM 12 HH2 Kme A 2 2.390 1.543 -0.143 1.00 0.00 H
ATOM 13 HH1 Kme A 2 3.908 0.553 -0.299 1.00 0.00 H
ATOM 14 HZ2 Kme A 2 1.741 0.264 1.756 1.00 0.00 H
ATOM 15 HZ1 Kme A 2 3.240 -0.502 1.846 1.00 0.00 H
ATOM 16 HE2 Kme A 2 1.683 -2.052 0.987 1.00 0.00 H
ATOM 17 HE1 Kme A 2 2.916 -1.654 -0.238 1.00 0.00 H
ATOM 18 HD2 Kme A 2 0.693 -1.756 -1.248 1.00 0.00 H
ATOM 19 HD1 Kme A 2 1.311 -0.088 -1.381 1.00 0.00 H
ATOM 20 HG2 Kme A 2 -0.125 0.640 0.510 1.00 0.00 H
ATOM 21 HG1 Kme A 2 -0.633 -1.065 0.821 1.00 0.00 H
ATOM 22 HB2 Kme A 2 -1.688 -1.156 -1.457 1.00 0.00 H
ATOM 23 HB1 Kme A 2 -1.159 0.523 -1.786 1.00 0.00 H
ATOM 24 HA Kme A 2 -3.560 0.401 -1.137 1.00 0.00 H
ATOM 25 H Kme A 2 -3.424 -1.490 0.288 1.00 0.00 H
ATOM 26 HW Kme A 2 -4.170 -0.209 1.058 1.00 0.00 H
ATOM 27 HW1 Kme A 2 -2.694 1.929 1.274 1.00 0.00 H
CONECT 1 2 25 26
CONECT 2 3 5 24
CONECT 3 4 4 27
CONECT 5 6 22 23
CONECT 6 7 20 21
CONECT 7 8 18 19
CONECT 8 9 16 17
CONECT 9 10 14 15
CONECT 10 11 12 13
END
error:
DEBUG: Max execution time tolerance is 3h
DEBUG: setResNameCheckCoords done
DEBUG: Net charge drift '0.000000'
==> ... charge set to 1
==> ... converting pdb input file to mol2 input file
DEBUG: /home/n_kristovsky/.conda/envs/topmol2/bin/obabel -ipdb Lysine_1M_rn_H_3D.pdb -omol2 -O Lysine_1M_rn_H_3D.mol2
==> * Babel OK *
==> Executing Antechamber...
DEBUG: /home/n_kristovsky/.conda/envs/topmol2/bin/antechamber -dr no -i Lysine_1M_rn_H_3D.mol2 -fi mol2 -o Lysine_1M_rn_H_3D_gas_amber.mol2 -fo mol2 -c gas -nc 1 -m 1 -s 2 -df 2 -at amber -pf n
DEBUG: No file left to be removed
ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR:
Welcome to antechamber 19.0: molecular input file processor.
Info: Finished reading file (Lysine_1M_rn_H_3D.mol2); atoms read (30), bonds read (26).
Running: /home/n_kristovsky/.conda/envs/topmol2/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/n_kristovsky/.conda/envs/topmol2/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p amber
Running: /home/n_kristovsky/.conda/envs/topmol2/bin/atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /home/n_kristovsky/.conda/envs/topmol2/dat/antechamber/ATOMTYPE_GAS.DEF
/home/n_kristovsky/.conda/envs/topmol2/bin/to_be_dispatched/antechamber: Fatal Error!
No Gasteiger parameter for atom (ID: 27, Name: H3, Type: DU).
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
DEBUG: /home/n_kristovsky/.conda/envs/topmol2/bin/parmchk2 -i Lysine_1M_rn_H_3D_gas_amber.mol2 -f mol2 -o Lysine_1M_rn_H_3D_AC.frcmod -p /tmp/parm10gaffff14SB.dat
ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Cannot open file (Lysine_1M_rn_H_3D_gas_amber.mol2) with mode (r).
No such file or directory
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[27], line 14
12 # ACTopol.parmchk
13 molecule.createACTopol()
---> 14 molecule.createMolTopol()
File ~/.conda/envs/topmol2/lib/python3.8/site-packages/acpype/topol.py:1116, in AbstractTopol.createMolTopol(self)
1112 def createMolTopol(self):
1113 """
1114 Create MolTopol obj.
1115 """
-> 1116 self.topFileData = open(self.acTopFileName).readlines()
1117 self.molTopol = MolTopol(
1118 self, # acTopolObj
1119 verbose=self.verbose,
(...)
1125 chiral=self.chiral,
1126 )
1127 if self.outTopols:
FileNotFoundError: [Errno 2] No such file or directory: 'Lysine_1M_rn_H_3D_AC.prmtop'
Good afternoon!
I am working on the parameterization of non-standard amino acids and have encountered an issue when generating an ITP file. At some point, one of the nitrogen atoms is assigned the atom type DU, and three protons (hydrogens) bound to it are also given the DU type. However, if I manually provide the PDB to Antechamber, all atom types are correct.
Do you have any ideas what might be causing this?
Here are examples of my code:
My pdb:
error: