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Dear Gromacs users
I need your kind suggestions on the problem I’m facing as below:-
I have a small ligand molecule for which I used acepype to generate topology. I want to use amber-99SB-ILDN forcefield for the protein so I added this forcefield into my local directory and followed the procedure mentioned in http://manual.gromacs.org/current/how-to/topology.html
However, I get the following error:-
ERROR 1 [file ffbonded.itp, line 676]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
I looked for the error and got that there is some duplication to the parameters which already exist in forcefield. After removing these bonded interactions ; bondtypes, angletypes and dihedraltypes I get a new error:-
ERROR 1 [file topol.top, line 16431]:
No default Bond types
ERROR 142 [file topol.top, line 73819]:
No default Proper Dih. types
I am not getting if 1 thing; GAFF parameters which I obtained from acepype have lowercase naming and different atomtypes, If these parameters exiist in forcefiled how can I recognise for each parameter.
Could you please help me to fix this problem.
Thanks in advance.