[AMBER] WARNING: There is a bond of 8.894214 angstroms between

From: Hyma vathi <hymavathi.niper.gmail.com>
Date: Mon, 26 Apr 2010 18:19:30 +0900

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)

Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education and Research(NIPER),
AMBER mailing list
Received on Mon Apr 26 2010 - 02:30:07 PDT
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