On Tue, Aug 20, 2024, Simran Modi via AMBER wrote:
>I have generated the ligand library for my ligand file but it is still
>not working. I have been following the tutorial for simulating a
>pharmaceutical compound. The process goes well until the generation of
>ligand library. When it comes to the complex part, the process gives fatal
>error showing that there is problem is atom bond order. The error file I
>am attaching herewith. Please help me with this. I am also attaching the
>complex file.
The error you seem to get shows this:
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
So, one of your bond commands to tleap is trying to create a bond between
atoms that do not exist in your system. The leap.log file is a better thing
to look at here, since it will tell you exactly which bond command is
causing the problem. Re-run tleap manually, and use the desc command
(before the bond command) to see the internal atom names and residue numbers
in your system.
...good luck...dac
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Received on Tue Aug 20 2024 - 09:30:02 PDT
