Try stripping out the hydrogens and just allowing tleap/sleap to fill them
in. You can strip waters via reduce:
reduce -Trim S_001009.pdb > S_001009_noh.pdb
The only atoms I've seen that have naming problems are hydrogens so this
should work.
HTH,
Jason
On Mon, Oct 3, 2011 at 1:30 PM, Asmita Gupta <asmita4des.gmail.com> wrote:
> This is the protocol i am following...i tried to follow the solution
> suggested by dac, still i am getting the same error:
>
> tleap -f leaprc.ff10
> rna=loadpdb "S_001009.pdb"
> addions rna Na+ 0
> solvatebox rna TIP3PBOX 12.0
>
> i am attaching the full PDB file which i am using. what is going wrong
> here?
>
> On Mon, Oct 3, 2011 at 9:33 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Mon, Oct 03, 2011, Asmita Gupta wrote:
> > >
> > > I am new to Amber. I am trying to generate prmtop and inpcrd files by
> > using
> > > saveamberparm but getting this error message again and again:
> > >
> > > FATAL: Atom .R<RG5 1>.A<H02' 33> does not have a type.
> >
> > You don't say what force field you are using. But in general, you can
> use
> > the
> > "list" command in tleap to see what residues are loaded, and the "desc"
> > command to find out atom names. For example:
> >
> > tleap -f leaprc.ff10
> > list <= shows that RNA residues are named, A,G,C,U
> > desc G.1 <= shows the atom names for residue "G"
> >
> > Amber tries to interpret new and old residue and atom names, but is not
> > foolproof. My best guess is that you are using a version 3 PDB file for
> > the
> > RNA, but are loading an older Amber library (e.g. ff99SB, but basically
> > anything other than ff10) which was formatted for PDB version 2.
> >
> > The PDB, in its infinite wisdom, changed the hydroxyl proton at the 2'
> > position from "HO'2" in version 2 to "HO2'" in version 3. The amber
> leaprc
> > files are *supposed* to make this change, but may not be doing so in all
> > cases. Unfortunately, without knowing the actual commands you used, it's
> > hard to be very helpful about the exact solution, but the general method
> > outlined here should enable you to resolve problems like these.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 03 2011 - 11:00:04 PDT
