Dear all,
Good morning. I am trying to build a ligand parameter file but running into
contant errors. I need help in understanding the errors as I am not sure
where they are coming from.
I obtained a docked structure that I sent to the RED server for determining
the charges. when I want to run it into tleap to create the topology and
rst7 file.it gives me the error "Possible open valence". after looking on
the internet, I found I can turnoff the acdoctor and can do the .lib file
by using the frcmod.known file from the server. When I want to build the
p.prmtop and .rst7 files, it gives me the error
................................
Building proper torsion parameters.
Error: ** No torsion terms for ce-cf-ca-ca
Error: ** No torsion terms for ce-cf-ca-ca
Error: ** No torsion terms for ha-cf-ca-ca
Error: ** No torsion terms for ha-cf-ca-ca
Building improper torsion parameters.
total 5 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
..............................................................................................
I checked the error in the list archive where they say to build the frcmod
file using parmchk.
When I run that I get
> parmchk -i ligand5.mol2 -f mol2 -o ligand5.frcmod
Error: Error from the parser: syntax error
...............................
I checked back its usage in the manual, I could not find where the problem
is.
Now my question is
1) what are these torsion term errors? when I checked the frcmod file,
there are no "ce" and "cf" carbon atoms. are these some general terms?
2) when i want to run the parmchk, what is the syntax error. is it a wrong
command line?
I am using Amber18 and AmberTools18 in WSL installed in ASUS laptop with
AMD Ryzen5 processor.
Your help is really appreciated.
Thank you
Ayesha Fatima
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Received on Fri Nov 06 2020 - 00:30:03 PST
