AMBER Archive (2008)

Subject: AMBER: sleap - TER-card

From: In Hee Park (
Date: Wed Jun 25 2008 - 14:14:39 CDT


I am switching to use sleap of amberTools instead of tleap in order to
utilize the new command "fastbld" for solvating a holo structure with
a docked small molecule.

There is no problem in producing prmtop/inpcrd/pdb for the solvated
system via "savemaberparms" and "savepdb". But TER-card is not added
between WAT residues, so that I cannot use "ambpdb" command correctly
to double check the pdb structure back from prmtop/inpcrd. While the
crystal waters - HOH residues - are separated by TER card, the
solvated WAT residues are not separated correctly by TER.

$ ambpdb -p prmtop < inpcrd > pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/22/06 Time = 12:10:21
At line 349 of file _ambpdb.f
Fortran runtime error: Bad value during integer read

Has anyone gotten any problem with sleap?

In-Hee Park
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