On Thu, Jan 24, 2013, Stefan Knippenberg wrote:
>
> Thanks for your suggestion about using ptraj via rst and then ambpdb,
> but it does not help.
>
> There is probably an issue the way I mention the .mol2 for the
> non-standard residu in tleap. Is it enough to say "loadmol2
> mol.mol2"? What don't I understand here?
>
> tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> mol = loadmol2 mol.mol2
> loadamberparams test.frcmod
> gaff = loadamberparams gaff.dat
> complex = loadpdb test.pdb
The "list" and "desc" commands should help. Use "list" to find out what tleap
thinks the residue names are, and "desc" to poke around inside those.
>
> and then we get:
>
> Created a new atom named: H within residue: .R<0 1>
You still seem to have a residue named "0" in your pdb file; is this really
what the residue is called in your previous prmtop file? Is it what the
residue is called in the mol2 file?
The message above says that there is an atom in the pdb file (residue
name/atom name pair) that does not exist in any library you have loaded. By
whatever means necessary, you have to make the pdb file names match those in
the libraries.
...dac
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Received on Thu Jan 24 2013 - 07:00:02 PST
