AMBER Archive (2006)

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

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Mon May 22 2006 - 11:49:46 CDT

This looks normal, since you have 200 frames there is no 201st frame to
read. Ptraj usually gives this error when it reaches the end of a file.
It can be confusing sometimes.

I hope this helps,

Asim

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. 

-- 
Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560

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