[AMBER] Problem on making inpcrd file

From: 肖立 <xiaoli19871216.gmail.com>
Date: Sun, 27 Jul 2014 13:06:34 -0700

    I use the amber14 tleap to generate an inpcrd file. I shows the
following message:
Checking Unit.
WARNING: There is a bond of 0.284304 angstroms between:
------- .R<NAP 262>.A<C1B 12> and .R<NAP 262>.A<N9A 13>
WARNING: There is a bond of 0.255071 angstroms between:
------- .R<NAP 520>.A<C1B 12> and .R<NAP 520>.A<N9A 13>
WARNING: The unperturbed charge of the unit: -0.993997 is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 1492 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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

    CTYR 2
    NAP 2
    NSER 2
    OCT 1
    WAT 11317
 (no restraints)
The inpcrd file is not generated right. It misses several coordinate
information as well as the box information.

I'm wondering if anyone can tells me why?

Thanks a lot!

Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Sun Jul 27 2014 - 13:30:02 PDT
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