Hi,
I am trying a simulate a protein with NAD+. I renamed NAD residue name as NDP in the pdb file. I am using amber12.0.
I applied the following commands
1) tleap -f leaprc.ff99SB
2) source leaprc.gaff
3) loadamberparams frcmod.NAD+
4) loadoff NAD+.lib
5) complex = loadpdb 2gdz_nad.pdb
Created a new atom named: PA within residue: .R<NDP 266>
Created a new atom named: O1A within residue: .R<NDP 266>
Created a new atom named: O2A within residue: .R<NDP 266>
Created a new atom named: O5B within residue: .R<NDP 266>
Created a new atom named: C5B within residue: .R<NDP 266>
Created a new atom named: C4B within residue: .R<NDP 266>
Created a new atom named: O4B within residue: .R<NDP 266>
Created a new atom named: C3B within residue: .R<NDP 266>
Created a new atom named: O3B within residue: .R<NDP 266>
Created a new atom named: C2B within residue: .R<NDP 266>
Created a new atom named: O2B within residue: .R<NDP 266>
Created a new atom named: C1B within residue: .R<NDP 266>
Created a new atom named: N9A within residue: .R<NDP 266>
Created a new atom named: C8A within residue: .R<NDP 266>
Created a new atom named: N7A within residue: .R<NDP 266>
Created a new atom named: C5A within residue: .R<NDP 266>
Created a new atom named: C6A within residue: .R<NDP 266>
Created a new atom named: N6A within residue: .R<NDP 266>
Created a new atom named: N1A within residue: .R<NDP 266>
Created a new atom named: C2A within residue: .R<NDP 266>
Created a new atom named: N3A within residue: .R<NDP 266>
Created a new atom named: C4A within residue: .R<NDP 266>
Created a new atom named: PN within residue: .R<NDP 266>
Created a new atom named: O2N within residue: .R<NDP 266>
Created a new atom named: O1N within residue: .R<NDP 266>
Created a new atom named: O5D within residue: .R<NDP 266>
Created a new atom named: C5D within residue: .R<NDP 266>
Created a new atom named: C4D within residue: .R<NDP 266>
Created a new atom named: O4D within residue: .R<NDP 266>
Created a new atom named: C3D within residue: .R<NDP 266>
Created a new atom named: O3D within residue: .R<NDP 266>
Created a new atom named: C2D within residue: .R<NDP 266>
Created a new atom named: O2D within residue: .R<NDP 266>
Created a new atom named: C1D within residue: .R<NDP 266>
Created a new atom named: N1N within residue: .R<NDP 266>
Created a new atom named: C2N within residue: .R<NDP 266>
Created a new atom named: C3N within residue: .R<NDP 266>
Created a new atom named: C7N within residue: .R<NDP 266>
Created a new atom named: O7N within residue: .R<NDP 266>
Created a new atom named: N7N within residue: .R<NDP 266>
Created a new atom named: C4N within residue: .R<NDP 266>
Created a new atom named: C5N within residue: .R<NDP 266>
Created a new atom named: C6N within residue: .R<NDP 266>
Added missing heavy atom: .R<NDP 266>.A<P1 1>
Added missing heavy atom: .R<NDP 266>.A<C1 5>
Added missing heavy atom: .R<NDP 266>.A<O7 23>
Added missing heavy atom: .R<NDP 266>.A<O1 2>
Added missing heavy atom: .R<NDP 266>.A<O2 3>
Added missing heavy atom: .R<NDP 266>.A<C2 6>
Added missing heavy atom: .R<NDP 266>.A<P2 24>
Added missing heavy atom: .R<NDP 266>.A<C3 8>
Added missing heavy atom: .R<NDP 266>.A<O4 7>
Added missing heavy atom: .R<NDP 266>.A<O10 27>
Added missing heavy atom: .R<NDP 266>.A<O8 25>
Added missing heavy atom: .R<NDP 266>.A<O9 26>
Added missing heavy atom: .R<NDP 266>.A<C4 10>
Added missing heavy atom: .R<NDP 266>.A<O5 9>
Added missing heavy atom: .R<NDP 266>.A<C5 12>
Added missing heavy atom: .R<NDP 266>.A<C11 28>
Added missing heavy atom: .R<NDP 266>.A<O6 11>
Added missing heavy atom: .R<NDP 266>.A<N1 13>
Added missing heavy atom: .R<NDP 266>.A<C12 29>
Added missing heavy atom: .R<NDP 266>.A<C6 14>
Added missing heavy atom: .R<NDP 266>.A<C10 22>
Added missing heavy atom: .R<NDP 266>.A<O11 30>
Added missing heavy atom: .R<NDP 266>.A<C13 31>
Added missing heavy atom: .R<NDP 266>.A<N2 15>
Added missing heavy atom: .R<NDP 266>.A<C7 16>
Added missing heavy atom: .R<NDP 266>.A<N5 21>
Added missing heavy atom: .R<NDP 266>.A<C15 35>
Added missing heavy atom: .R<NDP 266>.A<C14 33>
Added missing heavy atom: .R<NDP 266>.A<O12 32>
Added missing heavy atom: .R<NDP 266>.A<C8 17>
Added missing heavy atom: .R<NDP 266>.A<C9 20>
Added missing heavy atom: .R<NDP 266>.A<N6 36>
Added missing heavy atom: .R<NDP 266>.A<O13 34>
Added missing heavy atom: .R<NDP 266>.A<N4 19>
Added missing heavy atom: .R<NDP 266>.A<N3 18>
Added missing heavy atom: .R<NDP 266>.A<C21 44>
Added missing heavy atom: .R<NDP 266>.A<C16 37>
Added missing heavy atom: .R<NDP 266>.A<C20 43>
Added missing heavy atom: .R<NDP 266>.A<C17 38>
Added missing heavy atom: .R<NDP 266>.A<C19 42>
Added missing heavy atom: .R<NDP 266>.A<C18 39>
Added missing heavy atom: .R<NDP 266>.A<N7 41>
Added missing heavy atom: .R<NDP 266>.A<O14 40>
total atoms in file: 2082
Leap added 2126 missing atoms according to residue templates:
44 Heavy
2082 H / lone pairs
The file contained 43 atoms not in residue templates
6) saveamberparm complex 2gdz.prmtop 2gdz.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -5.000102 is not zero.
FATAL: Atom .R<NDP 266>.A<PA 73> does not have a type.
FATAL: Atom .R<NDP 266>.A<O1A 74> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I appreciate any help/suggestion in this regard.
Thanks and regards,
Latha.
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UT Southwestern Medical Center
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Received on Wed Dec 11 2013 - 15:00:03 PST
