On Wed, Feb 20, 2013 at 1:14 PM, 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?
>
Can you attach your prmtop? (and the files/commands you used to generate
it)?
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 20 2013 - 10:30:03 PST
