Hi,
On Mon, Aug 5, 2013 at 1:41 PM, Hailin Huang
<hailin.huang.my.liu.edu<javascript:;>>
wrote:
> Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> Warning: Could not determine atomic number from name [DX1 ]
Are you sure you are supposed to have atoms in your system with masses of
3.0? Unless they're some isotope like tritium this (as well as the atom
names themselves) seems strange. How did you create this topology?
-Dan
> Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> Warning: Could not determine atomic number from name [DY1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> Warning: Could not determine atomic number from name [DY2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> Warning: Could not determine atomic number from name [DX2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> Warning: Could not determine atomic number from name [DZ1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> Warning: Could not determine atomic number from name [DZ2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> Warning: Could not determine atomic number from name [DX1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> Warning: Could not determine atomic number from name [DY1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> Warning: Could not determine atomic number from name [DY2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> Warning: Could not determine atomic number from name [DX2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> Warning: Could not determine atomic number from name [DZ1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> Warning: Could not determine atomic number from name [DZ2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> Warning: Could not determine atomic number from name [DX1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> Warning: Could not determine atomic number from name [DY1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> Warning: Could not determine atomic number from name [DY2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> Warning: Could not determine atomic number from name [DX2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> Warning: Could not determine atomic number from name [DZ1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> Warning: Could not determine atomic number from name [DZ2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> Warning: Could not determine atomic number from name [DX1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> Warning: Could not determine atomic number from name [DY1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> Warning: Could not determine atomic number from name [DY2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> Warning: Could not determine atomic number from name [DX2 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> Warning: Could not determine atomic number from name [DZ1 ]
> Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> Warning: Could not determine atomic number from name [DZ2 ]
> [trajin ../prod113TNP-with2ADP2MG.mdcrd]
> [prod113TNP-with2ADP2MG.mdcrd] contains 2500 frames.
> [trajin ../prod123TNP-with2ADP2MG.mdcrd]
> [prod123TNP-with2ADP2MG.mdcrd] contains 2500 frames.
> [autoimage]
> AUTOIMAGE: To box center based on center of mass, anchor is first
> molecule.
> [trajout 3TNP-with2ADP2MG-prod-51-60ns.mdcrd netcdf]
> [run]
>
>
> How do I fix this issue? Any help would be greatly appreciated.
>
> Thanks,
> Richard
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 05 2013 - 14:00:02 PDT
