On Tue, Dec 20, 2022, Bruna Schuck de Azevedo via AMBER wrote:
>
>I want to do a simulation where NADPH is one of the ligands.
>
>When I try to run tleap, I get a warning:
You don't say what commands you gave to tleap. But it may just be that the
name of the residue in the PDB file (NPD) doesn't match the name of the
residue in the nadph.prep file.
After loading the prep file, use the "list" command to see what residues are
loaded. Basically, the atom and residue names in the library you load must
match exactly those in your pdb file.
>Unknown residue: NPD number: 0 type: Terminal/last
>Creating new UNIT for residue: NPD sequence: 3001
Above indicates that tleap doesn't know anything about an "NPD" residue.
The prep file you attached has "NPH" as the residue name. So, you probably
need to edit either the prep file or the PDB file.
....good luck...dac
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Received on Wed Dec 21 2022 - 06:30:02 PST
