You should use AmberTools 12 (free download from
http://ambermd.org) to
prepare your topology file instead of Amber 9. The errors you are
receiving are a result of a change in the PDB naming standard for RNA
residue names and atom names in nucleic acid residues. As a result, the
names in the PDB file do not match the names in the Amber 9 force field
residue template libraries.
Using tleap from AmberTools 12 has two advantages. First, the new naming
convention is supported (and we attempt to support older PDB atom/residue
naming as well, but I can't speak on how robust support is). Second, there
are newer, and likely better, force fields available to treat nucleic acids
(and getting the force field right is quite important for nucleic acids).
Good luck,
Jason
On Mon, Feb 25, 2013 at 7:25 AM, esmaeel azadian
<esmaeel_azadian.yahoo.com>wrote:
>
>
> Hi...
> I would like to do an molecular dynamics simulation study of RNA through
> Amber 9. Somebody advise me to use of leaprc.rna.ff02.
> But now I couldn't get the prmtop and inpcrd files and there is an error
> like this when I uses tleap :
>
> Total vdw box size: 90.530 132.178 125.221 angstroms.
> Volume: 1498401.380 A^3
> Mass > 787141.116 amu, Density > 0.872 g/cc
> (type - hence mass - of one or more atoms could not be found)
> Added 41581 residues.
> Checking Unit.
> FATAL: Atom .R<RG5 1>.A<HO5' 33> does not have a type.
> FATAL: Atom .R<RG5 1>.A<H5' 34> does not have a type.
> FATAL: Atom .R<RG5 1>.A<H5'' 35> does not have a type.
> FATAL: Atom .R<RG 2>.A<OP1 35> does not have a type.
> FATAL: Atom .R<RG 2>.A<OP2 36> does not have a type.
> FATAL: Atom .R<RG 2>.A<H5' 37> does not have a type.
> FATAL: Atom .R<RG 2>.A<H5'' 38> does not have a type.
> FATAL: Atom .R<RU 3>.A<OP1 31> does not have a type.
> FATAL: Atom .R<RU 3>.A<OP2 32> does not have a type.
> FATAL: Atom .R<RU 3>.A<H5' 33> does not have a type.
> FATAL: Atom .R<RU 3>.A<H5'' 34> does not have a type.
> FATAL: Atom .R<RG 4>.A<OP1 35> does not have a type.
> FATAL: Atom .R<RG 4>.A<OP2 36> does not have a type.
> FATAL: Atom .R<RG 4>.A<H5' 37> does not have a type.
> FATAL: Atom .R<RG 4>.A<H5'' 38> does not have a type.
> FATAL: Atom .R<RA 5>.A<OP1 34> does not have a type.
> FATAL: Atom .R<RA 5>.A<OP2 35> does not have a type.
> FATAL: Atom .R<RA 5>.A<H5' 36> does not have a type.
> FATAL: Atom .R<RA 5>.A<H5'' 37> does not have a type.
> FATAL: Atom .R<RU 6>.A<OP1 31> does not have a type.
> FATAL: Atom .R<RU 6>.A<OP2 32> does not have a type.
> FATAL: Atom .R<RU 6>.A<H5' 33> does not have a type.
> FATAL: Atom .R<RU 6>.A<H5'' 34> does not have a type.
> FATAL: Atom .R<RA 7>.A<OP1 34> does not have a type.
> FATAL: Atom .R<RA 7>.A<OP2 35> does not have a type.
> FATAL: Atom .R<RA 7>.A<H5' 36> does not have a type.
> FATAL: Atom .R<RA 7>.A<H5'' 37> does not have a type.
> FATAL: Atom .R<RG 8>.A<OP1 35> does not have a type.
> .
> .
> .
> .
>
> FATAL: Atom .R<RC 108>.A<OP1 32> does not have a type.
> FATAL: Atom .R<RC 108>.A<OP2 33> does not have a type.
> FATAL: Atom .R<RC 108>.A<H5' 34> does not have a type.
> FATAL: Atom .R<RC 108>.A<H5'' 35> does not have a type.
> FATAL: Atom .R<RU 109>.A<OP1 31> does not have a type.
> FATAL: Atom .R<RU 109>.A<OP2 32> does not have a type.
> FATAL: Atom .R<RU 109>.A<H5' 33> does not have a type.
> FATAL: Atom .R<RU 109>.A<H5'' 34> does not have a type.
> FATAL: Atom .R<RA 110>.A<OP1 34> does not have a type.
> FATAL: Atom .R<RA 110>.A<OP2 35> does not have a type.
> FATAL: Atom .R<RA 110>.A<H5' 36> does not have a type.
> FATAL: Atom .R<RA 110>.A<H5'' 37> does not have a type.
> FATAL: Atom .R<RC3 111>.A<OP1 33> does not have a type.
> FATAL: Atom .R<RC3 111>.A<OP2 34> does not have a type.
> FATAL: Atom .R<RC3 111>.A<H5' 35> does not have a type.
> FATAL: Atom .R<RC3 111>.A<H5'' 36> does not have a type.
> FATAL: Atom .R<RC3 111>.A<HO3' 37> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
>
>
>
> Could you please give me some advises.
>
>
> -----------------------------------------------------------------------------------
>
> Esmaeel Azadian
>
> Master Student
> Laboratory of Systems Biology and Bioinformatics
> (LBB)
> Institute of Biochemistry and Biophysics, University of
> Tehran
> Tehran, Iran
> http://LBB.ut.ac.ir
> esmaeel_azadian.yahoo.com
>
>
> -----------------------------------------------------------------------------------
> _______________________________________________
> 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
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Received on Mon Feb 25 2013 - 05:30:04 PST
