I added the OH at the beginning of my pdb file.
But still there is 4 atoms not in residue template.
ATOM 1 OH OHEOHE 1
ATOM 2 P U A 1
ATOM 3 OP1 U A 1
ATOM 4 OP2 U A 1
ATOM 5 O5' U A 1
I used SimRNA web server for prediction of this tertiary RNA structure.
Best Regards
On Sun, 11/27/2016 08:44 AM, David A Case <david.case.rutgers.edu> wrote:
> On Sun, Nov 27, 2016, Mohaddeseh Habibzadeh wrote:
>
> > As you mentioned before, I upgrade the AmberTools.
> > And as you can see below I made one of the terminal oxygens on the 5' phosphate appear in an OHE residue:
> > FATAL: Atom .R<OHE 2>.A<O5' 1> does not have type.
>
> You have to make both the atom name and the residue name match between the PDB
> file and the library. The atom name of the oxygen in OHE is "OH" not "O5'"
>
> > ATOM 1 P U A 1
> > ATOM 2 OP1 U A 1
> > ATOM 3 OP2 U A 1
> > ATOM 4 O5' OHE A 1
> > ATOM 5 C5' U A 1
> > ATOM 6 C4' U A 1
> > ATOM 7 O4' U A 1
>
> Also, you would need to put the OHE residue before the the U residue.
>
> *However, you don't want to change the O5' atom! Your PDB file has a
> phosphate with only three oxygens attached to it. You need to leave the O5'
> oxygen alone, and add an extra (fourth) oxygen, with residue name OHE and atom
> name OH.
>
> (I would be curious to know where this PDB file comes from: I've seen this
> behavior before, but don't know its origin.)
>
> ...good luck....dac
>
>
> _______________________________________________
> 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 Nov 27 2016 - 10:30:03 PST
