Dear Amber users,
I was trying to simulate a complex of dna with Furamidine. I used tlep to create input files for sander. But it generated an error as follows.I can't figure out the error. Please help me. It is very urgent.
Added missing heavy atom: .R<BGF 25>.A<N2' 23>
Added missing heavy atom: .R<BGF 25>.A<C7' 21>
Added missing heavy atom: .R<BGF 25>.A<N1' 22>
Added missing heavy atom: .R<BGF 25>.A<C6' 20>
Added missing heavy atom: .R<BGF 25>.A<CB' 3>
Added missing heavy atom: .R<BGF 25>.A<CA' 4>
total atoms in file: 801
Leap added 12 missing atoms according to residue templates:
6 Heavy
6 H / lone pairs
The file contained 12 atoms not in residue templates
Since added/missing = extra, there is a high probability
of atoms with 'incorrect' names; you may want to
use addPdbAtomMap to map these names, or change in file
Checking Unit.
WARNING: The unperturbed charge of the unit: -24.000300 is not zero.
FATAL: Atom .R<BGF 25>.A<CB* 42> does not have a type.
FATAL: Atom .R<BGF 25>.A<CA* 43> does not have a type.
FATAL: Atom .R<BGF 25>.A<C6* 44> does not have a type.
FATAL: Atom .R<BGF 25>.A<C7* 45> does not have a type.
FATAL: Atom .R<BGF 25>.A<N1* 46> does not have a type.
FATAL: Atom .R<BGF 25>.A<N2* 47> does not have a type.
FATAL: Atom .R<BGF 25>.A<HB* 48> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2* 49> does not have a type.
FATAL: Atom .R<BGF 25>.A<H5* 50> does not have a type.
FATAL: Atom .R<BGF 25>.A<H6* 51> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1*1 52> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1*2 53> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 14:28:47 PDT
