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
Received on Mon Feb 25 2013 - 04:30:04 PST
