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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Received on Wed Feb 20 2013 - 10:30:02 PST
