Re: AMBER: ptraj

From: <pengyo.UMDNJ.EDU>
Date: Mon, 12 Apr 2004 17:22:26 -0400

Dr. Cheatham,
FOllowing your suggestion, I did ptraj again. Even for a single frame, ptraj
has been running for 30m and hasn't fininshed. Is is normal? The trajectory
file traj_all.crd is a combined one by using ptraj.
Thanks for your help,


Input file:
trajin traj_all.crd 1 1 1
#reference pfmrk_md_prod_ct6.rst.gz
trajout traj_test.crd nobox
center :1-308 mass origin
image origin center
rms first out rms_image_first.out: 1-308.CA
#rms reference out rms_image_last.out: 1-308.CA
strip :WAT

output file
Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of .type)...
Read in residue labels...
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Read in box information...
Checking coordinates: traj_all.crd

Quoting "Thomas E. Cheatham, III" <>:

> > I try to use ptraj to analyze my MD trajectory file, which is pretty
> big and
> > contains about 630 snapshots (one 308AA protein+9A water shell). Ptraj
> has
> > been running for 7531m and nothing is in the output file.Is this
> normal? I
> > guess something must be wrong. The program iniated normally and checked
> the
> > coordinates in the file "traj_all.crd.gz" and then stopped there.
> > Anybody has any idea?
> This does not sound like the correct behavior.
> > The command I typed is "ptraj file.prmtop <> ptraj.out"
> Better would be to grab the standard error information in the output
> file
> as well...
> ptraj file.prmtop < >& ptraj.out
> > trajin traj_all.crd.gz
> > reference pfmrk_md_prod_ct6.rst.gz
> It may be hanging on this reference command.
> > trajout traj_all_image_NOWAT.crd
> You probably want to specify "nobox" on the above line if you are
> stripping water (otherwise you will have to build a prmtop with box
> information but no water in order to continue with the stripped
> trajectory).
> > center:1-308 mass origin
> There should be a space before the :1-308 above.
> > image origin center
> > rms first out rms_image_first.out: 1-308.CA
> > rms reference out rms_image_last.out: 1-308.CA
> > strip:WAT
> There should be a space before the :WAT
> I would try (1) adding the spaces before the : in each case
> (2) Remove the references/ rms reference by commenting those lines out
> (with a #) and (0) try processing only one frame first
> trajin traj_all.crd.gz 1 1 1
> It should run quick and I have run much larger systems without problem.
> Good luck,
> \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy,
> Depts of
> | Medicinal Chemistry and of Pharmaceutics and Pharmaceutical
> Chemistry
> | Adjunct Asst Prof of Bioengineering; Center for High Performance
> Computing
> | University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT
> 84112
> |
> | (801) 587-9652; FAX: (801)
> 585-9119
> \ BPRP295A / INSCC 418

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Received on Mon Apr 12 2004 - 22:53:00 PDT
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