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 - 09:30:02 PDT
