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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Received on Sun May 21 2006 - 06:07:14 PDT
