log started: Sat Jul 21 18:54:20 2007

Log file: ./leap_GDP.log
> verbosity 2
Verbosity level: 2
> GDP_dat = loadamberparams GDP.dat
Loading parameters: ./GDP.dat
Reading force field mod type file (frcmod)
(UNKNOWN ATOM TYPE: O3)
> loadAmberPrep GDP.prep
Loading Prep file: ./GDP.prep
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
Loaded UNIT: GDP
> GDP_loaded = loadpdb ./GDP.pdb
Loading PDB file: ./GDP.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: GDP, Terminal/last, was not found in name map.)
  total atoms in file: 40
> saveamberparm GDP_loaded GDP_loaded.PARM GDP_loaded.INPCRD
Checking Unit.
WARNING: The unperturbed charge of the unit: -3.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  NC-CB-CB-N*
        atoms are: N3 C5 C4 N9
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
old PREP-specified impropers:
 <GDP 1>:  C8   C4   N9   C1* 
 <GDP 1>:  C5   N1   C6   O6  
 <GDP 1>:  C6   C2   N1   H1N 
 <GDP 1>:  C2   H21  N2   H22 
 <GDP 1>:  N7   N9   C8   H80 
 <GDP 1>:  N1   N3   C2   N2  
--Impropers:
  1	C1*<GDP> - C8<GDP> - N9<GDP> - C4<GDP>
  1	C2<GDP> - H21<GDP> - N2<GDP> - H22<GDP>
  1	C5<GDP> - O6<GDP> - C6<GDP> - N1<GDP>
  1	C6<GDP> - H1N<GDP> - N1<GDP> - C2<GDP>
  1	N1<GDP> - N2<GDP> - C2<GDP> - N3<GDP>
  1	N9<GDP> - H80<GDP> - C8<GDP> - N7<GDP>
 total 6 improper torsions applied
 6 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit