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
>
>
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Received on Mon Oct 03 2011 - 11:00:03 PDT
