On Fri, Sep 18, 2015, Atila Petrosian wrote:
>
> Then, for the protein-ligand complex (comp.pdb), I used following:
>
>
> $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03.r1
> > source leaprc.gaff
> > mods = loadamberparams lig_h.frcmod
> > loadoff lig_h.lib
> > comp = loadpdb comp.pdb
...
> Creating new UNIT for residue: LIG sequence: 546
> Created a new atom named: N within residue: .R<LIG 546>
> Created a new atom named: C within residue: .R<LIG 546>
I'm guessing that "comp.pdb" has a different residue name for the ligand than
is used in the lig_h.lib file. Double check both the .lib file and the .pdb
file to make sure that atom and residue names match up.
(Hard to be very specific here, since we don't what is in either of these
files. But you probably have to edit the "comp.pdb" file to make the residue
and atom names match those in your library file.)
....dac
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Received on Fri Sep 18 2015 - 06:30:03 PDT
