On Tue, Jun 14, 2011, Antonija Tomić wrote:
>
> This is the tleap script that I have been using:
>
> source leaprc.ff03
> loadamberparams parm99.dat
> loadamberparams gaff.dat
This is a very odd set of commands: you are loading the ff03 force field,
but then over-riding the parameters with those from parm99.dat. This will
yield some very strange mixture of ff03 and ff99 that you almost certainly
don't want. I recommend you use either ff03 or ff10 (which is the same
as ff99SB for a protein). The gaff.dat file is not used --shouldn't do
any harm.
> enzSeq = { ILE VAL GLU SER TYR ILE GLY PHE ILE GLU SER TYR ARG ASP PRO
> PHE GLY SER ARG GLY GLU PHE GLU GLY PHE VAL ALA VAL VAL ASN LYS ALA
> MET SER ALA LYS PHE GLU ARG LEU VAL ALA SER ALA GLU GLN LEU LEU LYS
> GLU LEU PRO TRP PRO PRO THR PHE GLU LYS ASP LYS PHE LEU THR PRO ASP
> PHE THR SER LEU ASP VAL LEU THR PHE ALA GLY SER GLY ILE PRO ALA GLY
> ILE ASN ILE PRO ASN TYR ASP ASP LEU ARG GLN THR GLU GLY PHE LYS ASN
> VAL SER LEU GLY ASN VAL LEU ALA VAL ALA TYR ALA THR GLN ARG GLU LYS
> LEU THR PHE LEU GLU GLU ASP ASP LYS ASP LEU TYR ILE LEU TRP LYS GLY
> PRO SER PHE ASP VAL GLN VAL GLY LEU HID GLU LEU LEU GLY HID GLY SER
> GLY LYS LEU PHE VAL GLN ASP GLU LYS GLY ALA PHE ASN PHE ASP GLN GLU
> THR VAL ILE ASN PRO GLU THR GLY GLU GLN ILE GLN SER TRP TYR ARG SER
> GLY GLU THR TRP ASP SER LYS PHE SER THR ILE ALA SER SER TYR GLU GLU
> CYS ARG ALA GLU SER VAL GLY LEU TYR LEU CYS LEU HIE PRO GLN VAL LEU
> GLU ILE PHE GLY PHE GLU GLY ALA ASP ALA GLU ASP VAL ILE TYR VAL ASN
> TRP LEU ASN MET VAL ARG ALA GLY LEU LEU ALA LEU GLU PHE TYR THR PRO
> GLU ALA PHE ASN TRP ARG GLN ALA HIE MET GLN ALA ARG PHE VAL ILE LEU
> ARG VAL LEU LEU GLU ALA GLY GLU GLY LEU VAL THR ILE THR PRO THR THR
> GLY SER ASP GLY ARG PRO ASP ALA ARG VAL ARG LEU ASP }
OK..this is the problem. Strings in LEaP are limited to 1069 characters,
and your string is longer than this. [Of course, the C++ supporters can now
flood the list with comments about how to better avoid string overflows.]
I'm looking into seeing if just increasing the string size would correct
the problem, but a more basic question is this: why are you using
loadPdbUsingSeq rather than loadPdb itself? [My personal view is that the
loadPdbUsingSeq command should probably be deep-sixed -- we should ask
users to edit the pdb file if they need to change the sequence. But people
that make use of this command might want to chime in here.] But see if
you can just use loadPdb instead.
...regards...dac
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Received on Tue Jun 14 2011 - 06:30:03 PDT
