Hi Bill,
it looks like this, true.
Could you, please, check the list of files I'm downloading in leap, just
to be sure that I'm not missing something important, which maybe could
cause problems:
------------------------------------------------
Welcome to LEaP!
Sourcing: /data/bioinfp/sergeys/AmberMy/glyc_leaprc
Log file: ./leap.log
Loading parameters: /apps/bioinfp/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /apps/bioinfp/amber10/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading parameters: /data/bioinfp/sergeys/AmberMy/modified.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading library: /apps/bioinfp/amber10/dat/leap/lib/ions94.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/solvents.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/all_amino03.lib
----- Source: /apps/bioinfp/amber10/dat/leap/cmd/leaprc.GLYCAM_06
----- Source of /apps/bioinfp/amber10/dat/leap/cmd/leaprc.GLYCAM_06 done
Loading parameters: /apps/bioinfp/amber10/dat/leap/parm/GLYCAM_06c.dat
Reading title:
GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
Loading Prep file: /apps/bioinfp/amber10/dat/leap/prep/GLYCAM_06.prep
Loading library: /apps/bioinfp/amber10/dat/leap/lib/GLYCAM_amino_06.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/GLYCAM_aminoct_06.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/GLYCAM_aminont_06.lib
Loading library: /apps/bioinfp/amber10/dat/leap/lib/solvents.lib
-----------------------------
Thank you!
Sergey
Bill Ross wrote:
>>> ** Warning: No sp2 improper torsion term for CG-H1-CG-OH
>>> atoms are: C3 H2 C2 O2
>>> ** Warning: No sp2 improper torsion term for CG-H1-CG-CG
>>> atoms are: C3 H2 C2 C1
>>> ** Warning: No sp2 improper torsion term for CG-OH-CG-CG
>>> atoms are: C3 O2 C2 C1
>>> ... and so on
>>>
>>> What wrong I could do to get this or should I ignore these warnings?
>>>
>> Warnings are not errors: Usually, you can proceed... However in your =20
>> case, I do not understand why a sp2 atom is found among the =20
>> CG-H1-CG-OH atom types for instance...
>>
>> more $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06
>> [...]
>> addAtomTypes{
>> { "CG" "C" "sp3" }
>> { "H1" "H" "sp3" }
>> { "OH" "O" "sp3" }
>> }
>>
>> None of these atoms are sp2 but sp3. right ?
>>
>
> I believe what leap is calling sp2 may be any atom with 3 atoms
> bonded to it. Does this apply here?
>
> Bill
>
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Received on Mon Jul 06 2009 - 09:52:16 PDT
