Thanks for the help!
On Sun, Mar 13, 2011 at 4:55 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Chris,
>
> Ben is exactly correct, but I'll add to it some. Leap works based on force
> field templates, such as the OFF library files that Ben pointed you to (You
> can see a description of this file format on
> http://ambermd.org/formats.htmlfor both OFF files and amber Prep
> files); so the atom names in your PDB must
> match the atom names provided in the template files for those residues.
>
> The atom naming scheme in LEaP follows the atom naming scheme found in the
> current version of the PDB standard (which is obviously intentional). This
> makes sure that most standard PDBs that don't have specialized cofactors of
> any kind will work without any modification. This leads me to believe that
> you got your PDB file somewhere else (or had another program add hydrogen
> atoms to it).
>
> The easiest way to solve this is, as Ben said, strip H atoms from your PDB
> file and let LEaP add them back. You can do this via the program "reduce"
> using the -Trim flag.
>
> reduce -Trim input_pdb > output_pdb
>
> You can also use reduce to add the hydrogens back in if you don't want to
> use the locations LEaP puts them in (which are typically fine).
>
> Hope this helps,
> Jason
>
> On Sun, Mar 13, 2011 at 2:34 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
>
> > Hi Chris,
> >
> > On 13/03/2011, at 4:55 PM, Chris Bryant wrote:
> >
> > > Seems like it is all of them. Here is the file I am working with.
> Does
> > this answer your question?
> >
> > Thanks for the clarification. I don't think the problem is all the atoms;
> > for example, in your logs, it complains about ARG 361 HB1, ARG 361 HG1,
> ARG
> > 361 HD1, etc. Notably, however, HB2, HG2, HD2, etc. don't trigger the
> same
> > complaint. This is because, for example, LeAP expects hydrogens on CB in
> ARG
> > residues to be named HB2 and HB3, instead of HB1 and HB2 (and likewise
> for
> > hydrogens attached to other heavy atoms).
> >
> > If I understand correctly, LeAP expects very specific atom names in its
> > residues when assigning atom types. If your atoms aren't named according
> to
> > the entries in the residue topology libraries, it won't be able to
> address
> > them.
> >
> > The official atom naming scheme can be found in the file:
> >
> > $AMBERHOME/dat/leap/lib/all_amino94.lib (for intra-chain amino acids)
> > $AMBERHOME/dat/leap/lib/all_aminoct94.lib (for C-terminal amino acids)
> > $AMBERHOME/dat/leap/lib/all_aminont94.lib (for N-terminal amino acids)
> >
> > One possible approach is to fix the hydrogen atom names by hand (for
> > example, in residue 361, replacing HB1 and HB2 with HB2 and HB3
> > respectively, and so on). However, I don't recommend this given that it's
> > very time-consuming. Another is to throw away all hydrogen atoms from
> your
> > PDB and let other programs add them for you. I think leap should be able
> to
> > add correctly named hydrogen atoms automatically given a heavy-atom
> > skeleton; if not, check out "reduce", which is bundled with AmberTools.
> >
> > Good luck!
> >
> > Ben
> >
> > --
> > For greater security, I support S/MIME encryption.
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 13 2011 - 16:00:01 PDT
