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
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Received on Mon Apr 26 2010 - 03:00:06 PDT
