Hi,
Do those flags actually exist in the topology file (i.e. does "grep
BONDS_WITHOUT_HYDROGEN prmtop" return any output)? If not, then the
topology is likely corrupted somehow, and it will help to debug
further if you specify what your exact input to leap was.
If they do exist, is cpptraj able to read the topology file?
-Dan
On Wed, Feb 20, 2013 at 11:14 AM, Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
> Dear all,
>
> I am trying to create a parameter file for protein-RNA system using xleap
> or tleap in AMBER12 using ff99SB and ff99bsc0.
> I can confirm that both tleap and xleap seems to run properly, no fatal
> error or unusual termination.
> However, the produced parameter file causes a segmentation fault with ptraj.
> I noticed that the size of the file
> is almost half the size of what is expected indicating the file is not
> complete, and when I checked the file using rdparm I see messages about
> missing flags at the end of the file:
>
> PRMTOP does not contain %FLAG BONDS_WITHOUT_HYDROGEN
> PRMTOP does not contain %FLAG ANGLES_INC_HYDROGEN
> PRMTOP does not contain %FLAG ANGLES_WITHOUT_HYDROGEN
> PRMTOP does not contain %FLAG DIHEDRALS_INC_HYDROGEN
> PRMTOP does not contain %FLAG DIHEDRALS_WITHOUT_HYDROGEN
> PRMTOP does not contain %FLAG EXCLUDED_ATOMS_LIST
> PRMTOP does not contain %FLAG HBOND_ACOEF
> PRMTOP does not contain %FLAG HBOND_BCOEF
> PRMTOP does not contain %FLAG HBCUT
> PRMTOP does not contain %FLAG AMBER_ATOM_TYPE
> PRMTOP does not contain %FLAG TREE_CHAIN_CLASSIFICATION
> PRMTOP does not contain %FLAG JOIN_ARRAY
> PRMTOP does not contain %FLAG IROTAT
> PRMTOP does not contain %FLAG SOLVENT_POINTERS
> PRMTOP does not contain %FLAG ATOMS_PER_MOLECULE
> PRMTOP does not contain %FLAG BOX_DIMENSIONS
> PRMTOP does not contain %FLAG RADIUS_SET
> PRMTOP does not contain %FLAG RADII
> PRMTOP does not contain %FLAG SCREEN
> Segmentation fault
>
> I should say that I never had such a problem before using previous versions
> of AMBER.
>
> Any idea what is the cause of this problem? And what is solution?
>
> Thanks in advance for your help.
>
> Regards,
> Ibrahim
>
>
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> AMBER.ambermd.org
> 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)
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Received on Wed Feb 20 2013 - 10:30:04 PST
