Hi,
On Wed, Jun 19, 2013 at 10:49 AM, Fabrício Bracht <fabracht1.gmail.com> wrote:
> Hello. I am experiencing some issues with ambertools 13 while trying to
> analyse different systems. The first system is a "normal" pmemd.cuda
> simulation of a protein in water. When I type the command cpptraj -i
> rmsd.ptraj -p HOH_wat.prmtop, I get the following error:
CPPTRAJ currently processes flags on the command line in order. This
means that what is happening is your input file (rmsd.ptraj) is being
read in before your topology file (HOH_wat.prmtop). However, since
some of your input depends on the topology file (namely the 'trajin'
command), it fails.
> Error: Atom 5311 was assigned a lower molecule # than previous atom.
> Error: This can happen if bond information is incorrect or missing.
> Error: Detected # of molecules is 7615. If this is incorrect and your
> Error: topology does not have bond information (e.g. PDB file), try
> Error: increasing the bond search cutoff offset (currently 0.200000).
> Error: e.g. 'parm HOH_wat.prmtop bondsearch <new offset>'
> Error: This can also happen if the atoms in your molecules are not
> Error: sequential (e.g. molecule 1 is atoms 1-4,10-14 and molecule 2
> Error: is atoms 5-9,15-20). This can be fixed using the 'setMolecules'
> Error: command in parmed.py.
> Error: Could not open parm HOH_wat.prmtop
As stated by the error message, this can be caused by either incorrect
bond information or if atoms are not sequential within your molecules
(I suspect the latter). Cpptraj requires that atoms in molecules be
sequential for speed (among other things). Did you try using the
'setMolecules' command in parmed.py?
> I didn't have any of this issues with ambertools 12. Please, let me know if
AmberTools 12 CPPTRAJ didn't do as much error checking as AmberTools
13 CPPTRAJ does, and would not have caught this problem.
-Dan
--
-------------------------
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 Jun 19 2013 - 10:30:04 PDT
