AMBER Archive (2006)

Subject: Re: AMBER: RE: trouble stripping waters with ptraj

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sat May 20 2006 - 12:10:24 CDT

did you use "nobox" when you wrote the stripped trajectory
from ptraj?

Adam Pelzer wrote:

>
> 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
>
> ------------------------------------------------------------------------
> Sneak preview the all-new Yahoo.com
> <http://us.rd.yahoo.com/evt=40762/*http://www.yahoo.com/preview>. It's
> not radically different. Just radically better.

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