For example, try to load your comp_sol.prmtop and comp_sol.inpcrd into VMD
and examine actual connectivity (this is reasonable when using Tleap; in
case of Xleap I suppose you could find any mistakes using graphical
interface).
If mistake takes place, you could build pdb of cofactor using just its
parameter files (after loading parameters in tleap you should get new UNIT
of your cofactor) and compare order and names with your pdb.
On Mon, Apr 26, 2010 at 1:55 PM, Hyma vathi <hymavathi.niper.gmail.com>wrote:
> But how will I get to know that the they are in order and match in pdb ?
>
> On Mon, Apr 26, 2010 at 6:33 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
>
> > Hello!
> > I suppose that atom order or atom names don't match in your pdb and in
> file
> > of cofactor topology, so you get wrong connectivity.
> >
> > On Mon, Apr 26, 2010 at 1:19 PM, Hyma vathi <hymavathi.niper.gmail.com
> > >wrote:
> >
> > > Dear Amber Users,
> > >
> > > I am trying to simulate a protein with a cofactor, when I was trying to
> > > save
> > > the prmtop file the following message has come. Can anyone please tell
> > how
> > > to sort out this problem. Thank you in advance.
> > >
> > > > saveamberparm comp comp_sol.prmtop comp_sol.inpcrd
> > > Checking Unit.
> > > WARNING: There is a bond of 8.894214 angstroms between:
> > > ------- .R<NAP 316>.A<O3B 18> and .R<NAP 316>.A<HO3 19>
> > >
> > > -- ignoring the warning.
> > >
> > > Building topology.
> > > Building atom parameters.
> > > Building bond parameters.
> > > Building angle parameters.
> > > Building proper torsion parameters.
> > > Building improper torsion parameters.
> > > old PREP-specified impropers:
> > > <NAP 316>: C5A N9A C4A N3A
> > > <NAP 316>: H2A N3A C2A N1A
> > > <NAP 316>: C5A N1A C6A N6A
> > > <NAP 316>: C6A HN6 N6A H9
> > > <NAP 316>: C4A C6A C5A N7A
> > > <NAP 316>: H8A N9A C8A N7A
> > > <NAP 316>: C1B C4A N9A C8A
> > > <NAP 316>: C1D C2N N1N C6N
> > > <NAP 316>: C3N H2N C2N N1N
> > > <NAP 316>: C7N C2N C3N C4N
> > > <NAP 316>: C3N N7N C7N O7N
> > > <NAP 316>: C7N HN7 N7N H10
> > > <NAP 316>: C3N C5N C4N H4N
> > > <NAP 316>: C4N C6N C5N H5N
> > > <NAP 316>: C5N H6N C6N N1N
> > > <ZST 317>: C17 O2 C18 O3
> > > <ZST 317>: C17 C3 C4 N2
> > > <ZST 317>: C8 C2 C3 C4
> > > <ZST 317>: C3 C7 C8 H8
> > > <ZST 317>: C8 C6 C7 H7
> > > <ZST 317>: C7 C5 C6 H6
> > > <ZST 317>: C6 C2 C5 H5
> > > <ZST 317>: C1 C3 C2 C5
> > > <ZST 317>: C2 N1 C1 O1
> > > <ZST 317>: C1 C9 N1 N2
> > > <ZST 317>: C9 N3 C10 S1
> > > <ZST 317>: C16 C11 C12 N3
> > > <ZST 317>: C12 C15 C16 H16
> > > <ZST 317>: C12 C13 C11 S1
> > > <ZST 317>: C11 C14 C13 H13
> > > <ZST 317>: C13 C15 C14 H14
> > > <ZST 317>: C19 C16 C15 C14
> > > total 1009 improper torsions applied
> > > 32 improper torsions in old prep form
> > > Building H-Bond parameters.
> > > Not Marking per-residue atom chain types.
> > > Marking per-residue atom chain types.
> > > (Residues lacking connect0/connect1 -
> > > these don't have chain types marked:
> > >
> > > res total affected
> > >
> > > CPHE 1
> > > NALA 1
> > > WAT 8025
> > > )
> > > (no restraints)
> > >
> > >
> > > --
> > > Hymavathi,
> > > MS(Pharm),
> > > Center for Pharmacoinformatics,
> > > National Institute of Pharmaceutical Education and Research(NIPER),
> > > Mohali,
> > > INDIA.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dmitry Nilov,
> > Lomonosov Moscow State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Hymavathi,
> MS(Pharm),
> Center for Pharmacoinformatics,
> National Institute of Pharmaceutical Education and Research(NIPER),
> Mohali,
> INDIA.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov,
Lomonosov Moscow State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 26 2010 - 04:00:05 PDT
