AMBER Archive (2006)

Subject: AMBER: RE: trouble stripping waters with ptraj

From: Adam Pelzer (yankeeswin314159_at_yahoo.com)
Date: Sat May 20 2006 - 11:00:12 CDT

Thank you very much for your advice. I fixed the problem with the prmtop file as you suggested, but I'm afraid that my troubles have persisted. Since I wanted to work with a mdcrd file that had both waters and counterions stripped, I initially tried creating a new prmtop file using xleap, in which I worked with the original pdb file but skipped adding water and counterions. I tried using this new prmtop file with a mdcrd file from which I had stripped the waters and counterions (using ptraj), but I received an error message saying:

Processing AMBER trajectory file sim_an_1000_water_stripped.mdcrd

Set 1 .................................................

Set 50 .................................................

Set 100 .................................................

Set 150 .................................................

Set 200

Set #201 appears corrupted (

49.453 27.539 40.4013)

This is very strange, because there shouldn't be a Set #201! My trajectory file has only 200 frames. I thought that perhaps it would work if I simply stripped water but not ions, so I created a prmtop file using rdparm from which I had stripped the waters, then I created a mdcrd file from which I had stripped the waters but not the ions, and I tried them together, with this result:

Processing AMBER trajectory file sim_an_1000_water_but_not_ions_stripped.mdcrd

Set 1 .................................................

Set 50 .................................................

Set 100 .................................................

Set 150 .................................................

Set 200

ERROR in readAmberTrajectory(): Set #201 is corrupted (

￿\^5￿￿?`s￿￿#X￿?}￿￿

￿d￿?3)...

Again, Set #201 should not exist. I don't know what I am doing wrong. Does anyone have any suggestions?

Thank you in advance for any advice--I very much appreciate it.

Adam

                        
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