> Could you, please, check the list of files I'm downloading in leap
I haven't used amber for years (I worked on leap for over 5 years
once), so am too out of date to comment on the files. Questions
that come to mind are: are the relevant atoms in protein or
glycam residues? Are atom types consistent across the two ff's?
Bill
>>> ** 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 - 09:55:37 PDT
