Hi, all:
I'm using tleap to generate prmtop and inpcrd for protein with rna, and
when loading it, it shows this kind of warning
Created a new atom named: 'H5' within residue: .R<RA 39>
Created a new atom named: 'HO2 within residue: .R<RA 39>
Created a new atom named: 'H5' within residue: .R<RA 40>
Created a new atom named: 'HO2 within residue: .R<RA 40>
Created a new atom named: 'H5' within residue: .R<RA 41>
Created a new atom named: 'HO2 within residue: .R<RA 41>
Created a new atom named: 'H5' within residue: .R<RA 42>
Created a new atom named: 'HO2 within residue: .R<RA 42>
Created a new atom named: 'H5' within residue: .R<RA 43>
Created a new atom named: 'HO2 within residue: .R<RA 43>
Created a new atom named: 'H5' within residue: .R<RA 44>
Created a new atom named: 'HO2 within residue: .R<RA 44>
Created a new atom named: 'H5' within residue: .R<RA 45>
Created a new atom named: 'HO2 within residue: .R<RA 45>
Created a new atom named: 'H5' within residue: .R<RA 46>
Created a new atom named: 'HO2 within residue: .R<RA 46>
Created a new atom named: 'H5' within residue: .R<RA 47>
Created a new atom named: 'HO2 within residue: .R<RA 47>
Created a new atom named: 'H5' within residue: .R<RA 48>
Created a new atom named: 'HO2 within residue: .R<RA 48>
Created a new atom named: 'H5' within residue: .R<RA 49>
Created a new atom named: 'HO2 within residue: .R<RA 49>
Created a new atom named: 'H5' within residue: .R<RA 50>
Created a new atom named: 'HO2 within residue: .R<RA 50>
Created a new atom named: 'H5' within residue: .R<RA 51>
Created a new atom named: 'HO2 within residue: .R<RA 51>
Created a new atom named: 'H5' within residue: .R<RA 52>
Created a new atom named: 'HO2 within residue: .R<RA 52>
Created a new atom named: 'H5' within residue: .R<RA 53>
Created a new atom named: 'HO2 within residue: .R<RA 53>
Created a new atom named: 'H5' within residue: .R<RA 54>
Created a new atom named: 'HO2 within residue: .R<RA 54>
Created a new atom named: 'H5' within residue: .R<RA 55>
Created a new atom named: 'HO2 within residue: .R<RA 55>
Created a new atom named: 'H5' within residue: .R<RA 56>
Created a new atom named: 'HO2 within residue: .R<RA 56>
Created a new atom named: 'H5' within residue: .R<RA3 57>
Created a new atom named: 'HO2 within residue: .R<RA3 57>
Created a new atom named: 'HO3 within residue: .R<RA3 57>
total atoms in file: 5622
Leap added 4002 missing atoms according to residue templates
and finally it failed to save a prmtop file with the error message:
FATAL: Atom .R<A 55>.A<'H5' 34> does not have a type.
FATAL: Atom .R<A 55>.A<'HO2 35> does not have a type.
FATAL: Atom .R<A 56>.A<'H5' 34> does not have a type.
FATAL: Atom .R<A 56>.A<'HO2 35> does not have a type.
FATAL: Atom .R<A3 57>.A<'H5' 35> does not have a type.
FATAL: Atom .R<A3 57>.A<'HO2 36> does not have a type.
FATAL: Atom .R<A3 57>.A<'HO3 37> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Can anyone tells me how to solve it?
Thank you
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Tue Jun 24 2014 - 18:00:02 PDT
