alanwilter
commented
1 year ago You need to check what is the net charge of you system. The sqm routine won't run it's telling you why: you have 721 electrons, this cannot be net charge 0. ACPYPE try to guess the net charge but this sometimes won't work.
Hi guys I have this problem, anyone can help me please?
ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.8.25 (c) 2022 AWSdS |
WARNING: no charge value given, trying to guess one... ==> ... charge set to 0 ==> ... converting pdb input file to mol2 input file ==> Babel OK ==> Executing Antechamber... ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Welcome to antechamber 21.0: molecular input file processor.
The atom type is set to gaff2; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl. Info: Finished reading file (Lig70.mol2); atoms read (120), bonds read (130). Info: Determining atomic numbers from atomic symbols which are case sensitive. Running: /home/sajad/acpype/acpype/amber21-11_linux/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Warning: The assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c (be cautious, using a large value of PSCUTOFF (>100) will significantly increase the computation time).
Running: /home/sajad/acpype/acpype/amber21-11_linux/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff2 Info: Total number of electrons: 721; net charge: 0 Info: The number of electrons is odd (721). Please check the total charge (-nc flag) and spin multiplicity (-m flag).
Running: /home/sajad/acpype/acpype/amber21-11_linux/bin/sqm -O -i sqm.in -o sqm.out /home/sajad/acpype/acpype/amber21-11_linux/bin/wrapped_progs/antechamber: Fatal Error! Cannot properly run "/home/sajad/acpype/acpype/amber21-11_linux/bin/sqm -O -i sqm.in -o sqm.out".
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Antechamber failed ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Cannot open file (Lig70_bcc_gaff2.mol2) with mode (r). No such file or directory ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Parmchk failed ERROR: Tleap failed ==> Removing temporary files... ERROR: ACPYPE FAILED: [Errno 2] No such file or directory: 'Lig70_AC.prmtop' Traceback (most recent call last): File "/home/sajad/acpype/acpype/cli.py", line 140, in init_main molecule.createMolTopol() File "/home/sajad/acpype/acpype/topol.py", line 1116, in createMolTopol self.topFileData = open(self.acTopFileName).readlines() FileNotFoundError: [Errno 2] No such file or directory: 'Lig70_AC.prmtop' Total time of execution: 1s