Make your atom names in pdb agree with the residue templates, or use an atom name map to do it automatically. Try 'help' in leap to see the list of cmds.
Bill
-------- Original message --------
From: 肖立 <xiaoli19871216.gmail.com>
Date:06/24/2014 5:31 PM (GMT-08:00)
To: AMBER Mailing List <AMBER.ambermd.org>
Subject: [AMBER] Problem in creating prmtop inpcrd file in leap
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 - 18:30:02 PDT
