GROMACS version: 4.0.7-Ubuntu-2020.1-1
GROMACS modification: No
Hi everyone!
I’m trying to simulate a system with a Janus MoSSe in gromacs, but I need the itp and top files to do the simulations. I tried to generate a topology with a gromacs version 4.0.7, I also tried to generate using acpype but it always gives an error.
In gromacs I tried like this:
~/packages/gromacs-4.0.7/bin/x2top -f old/unit-cell.pdb -o old/topologia.top -ff amber99sb
There are 25 name to type translations
Generating bonds from distances…
atom 6
Can not find forcefield for atom MO-1 with 0 bonds
Can not find forcefield for atom MO-2 with 0 bonds
Can not find forcefield for atom SE-3 with 0 bonds
Can not find forcefield for atom SE-4 with 0 bonds
Can not find forcefield for atom S-5 with 0 bonds
Can not find forcefield for atom S-6 with 0 bonds
Fatal error:
Could only find a forcefield type for 0 out of 6 atoms
And in acpype this error appears:
acpype -i unit.pdb -c user
.
.
.
Running: /home/gabriel/.local/lib/python3.8/site-packages/acpype/amber_linux/bin/sqm -O -i sqm.in -o sqm.out
/home/gabriel/.local/lib/python3.8/site-packages/acpype/amber_linux/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run “/home/gabriel/.local/lib/python3.8/site-packages/acpype/amber_linux/bin/sqm -O -i sqm.in -o sqm.out”.
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Cannot open file (unit_user_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: ‘unit_AC.prmtop’
Traceback (most recent call last):
File “/home/gabriel/.local/lib/python3.8/site-packages/acpype/cli.py”, line 138, in init_main
molecule.createMolTopol()
File “/home/gabriel/.local/lib/python3.8/site-packages/acpype/topol.py”, line 1115, in createMolTopol
self.topFileData = open(self.acTopFileName).readlines()
FileNotFoundError: [Errno 2] No such file or directory: ‘unit_AC.prmtop’
Total time of execution: 1s
Any suggestions or ways to get around this error? Should I try another way to get my topology?