mol2 files from my experience do not have HEAD and TAIL atom definitions, or
connect0 and connect1 (that is, it says nothing about the bonding to the
adjacent residues so tleap assumes that it does not bond at all). Before
you use the "saveoff" command in tleap to save your PHD library file, you
should, as Dave Case suggested, set the head and tail atoms.
Pick the atoms that you want to connect to adjacent residues and set them as
head and tail:
set PHD head PHD.1.atom_name
set PHD tail PHD.1.atom_name
This should fix it.
Good luck!
Jason
On Sat, Jan 8, 2011 at 11:59 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>
> Thank you so much.
>
> I compare phosphoaspartate library which I have created and psophoserine
> library
> from Amber
> parameter database, in my library there is connectivity prodblem.
>
> PHOSPHOSERINE library:-
>
> !entry.T1P.unit.childsequence single int
> 2
> !entry.T1P.unit.connect array int
> 1
> 17
> !entry.T1P.unit.connectivity table int atom1x int atom2x int flags
> 1 2 17
> 1 3 17
> 3 4 17
> 3 17 17
> 3 5 17
> 5 6 17
> 5 11 17
> 5 7 17
> 7 8 17
> 7 9 17
> 7 10 17
> 11 12 17
> 12 15 17
> 12 14 17
> 12 13 17
> 13 16 17
> 17 18 17
>
> and in PHOSPHOASPARTATE which I have created :-
>
> !entry.PHD.unit.childsequence single int
> 2
> !entry.PHD.unit.connect array int
> 0
> 0
> !entry.PHD.unit.connectivity table int atom1x int atom2x int flags
> 1 2 1
> 1 16 1
> 1 17 1
> 2 3 1
> 2 5 1
> 2 15 1
> 3 4 1
> 5 6 1
> 5 13 1
> 5 14 1
> 6 7 1
> 6 8 1
> 7 9 1
> 9 10 1
> 9 11 1
> 9 12 1
>
>
> Here what are these number 1, 17 in phosserine library i.e.
> entry.T1P.unit.connect array int
> 1
> 17
>
>
>
> How I can modify phosphoaspartate library?
>
> When I look sus.lib generated in tutorial
> http://ambermd.org/tutorials/basic/tutorial4b/
> connectivity in this library is also silmilar to pshosphoaspartate.
>
>
>
>
>
>
>
> > On Sat, Jan 08, 2011, Sangita Kachhap wrote:
> >>
> >> I edited the PDB file remove TER card. When load it to tleap
> >> with frcmod file and lib file tleap again adding TER card to thses
> position
> >
> > Something bad is happening....maybe your library doesn't have "head" and
> > "tail" atoms identified. If they are missing, you need to add them --
> compare
> > your modified library to the original ASP one. Or, look at the
> phosphoserine,
> > etc. residues in the contributed parameters database to see how they look
> > different from yours.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> With regard
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 08 2011 - 10:00:04 PST
