You should use the AMBER atom types rather than gaff when building your
modified residue. GAFF is more for small organic ligands, and no parameters
exist between gaff and amber atom types (you'd have to manually find those
and add them to an frcmod file). Maybe parmchk can do it, but I'd still
suggest using amber atom types instead.
Hope this helps,
Jason
On Sat, Jan 8, 2011 at 2:59 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Thanks for reply.
>
> Here I have before saveoff command
> set PHD head PHD.1.N
> set PHD tail PHD.1.O
>
> Then saveoff PHD.lib.
>
> Now when I am loading PDB file in which I have to add phosphate group with
> .frcmod
> and .lib file all going OK but when saving topology and coordinate file
> parameter file
> is not saving.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: C - n3
> Could not find bond parameter for: o - N
> Building angle parameters.
> Could not find angle parameter: O - C - n3
> Could not find angle parameter: C - n3 - c3
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: CT - C - n3
> Could not find angle parameter: o - N - H
> Could not find angle parameter: o - N - CT
> Could not find angle parameter: c1 - o - N
> Building proper torsion parameters.
> ** No torsion terms for O-C-n3-c3
> ** No torsion terms for O-C-n3-hn
> ** No torsion terms for O-C-n3-hn
> ** No torsion terms for CT-C-n3-c3
> ** No torsion terms for CT-C-n3-hn
> ** No torsion terms for CT-C-n3-hn
> ** No torsion terms for c1-o-N-H
> ** No torsion terms for c1-o-N-CT
> ** No torsion terms for c3-c1-o-N
> Building improper torsion parameters.
> total 582 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>
>
>
>
>
>
>
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 08 2011 - 12:30:04 PST
