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.
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Received on Mon Apr 26 2010 - 03:00:07 PDT
