Importing from Amber

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Jon Mujika
Importing from Amber

Dear ChemShell users,

I am trying to import a system from Amber using the following input file:

load_amber_coords inpcrd=prod.inpcrd prmtop=sys.prmtop coords=prod.c

energy energy=e coords=prod.c theory=dl_poly : [ list \
amber_prmtop_file=sys.prmtop \
scale14 = [ list [ expr 1 / 1.2 ] 0.5 ] \
use_pairlist = no \
save_dl_poly_files = yes \
list_option=full ]

set atom_charges [ list_amber_atom_charges ]
set res [ pdb_to_res "sys.pdb" ]

set fp [ open save_amb.chm w]
puts $fp "set atom_charges [ list $atom_charges ]"
puts $fp "set res [ list $res ]"
close $fp

But I get the next error:

~/chemsh-3.6.0/scripts/chemsh: line 276: 10964 Segmentation fault $app $args

Although looking at the FIELD file, it seems the system was imported correctly. I’ve used the same input successfully with other systems, but in this one there are some non-standard residues. Can it be this the source of the error? If it is, how should I proceed? I would appreciate any help.

Thanks in advance

Jon

tomkeal
tomkeal's picture
Hi Jon,

Hi Jon,

It's possible non-standard residues are triggering the problem, but in any case they shouldn't cause a segmentation fault. It looks like you're using Tcl-ChemShell 3.6 and the first thing I'd suggest is upgrading to v3.7 as we fixed several errors of this type in the latest version. If you email me direct I'll send you the download instructions.

Cheers,

Tom

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