AMBER Archive (2008)

Subject: Re: AMBER: Trajectory in "Sietraj"

From: Alfredo Quevedo (alfredoq_at_mail.fcq.unc.edu.ar)
Date: Tue Jun 03 2008 - 10:29:24 CDT

Dear Enrico and Florian, I changed the set MarTet_TMP_SIZE variable to
500000 and the calculation worked fine.
Thanks for the support!!
Best regards

Alfredo Quevedo

----- Original Message -----
From: "Purisima, Enrico" <Enrico.Purisima_at_cnrc-nrc.gc.ca>
To: <amber_at_scripps.edu>
Sent: Tuesday, June 03, 2008 11:39 AM
Subject: RE: AMBER: Trajectory in "Sietraj"

> Dear Alfredo,
>
> This error can arise from very large systems or for long extended unfolded
> proteins. How large is your system? You can try editing the sietraj.tcl
> file in the apps/sietraj directory. Change the value 200000 in the line
>
> set MarTet_TMP_SIZE 200000
>
> to 300000 or some larger number.
>
> The error can also be a side-effect of a mismatch between the prmtop and
> trajectory file. If you wish, you can send me a copy of your prmtop file
> and a few frames of your trajectory file and I can look into the error.
> (If these are big files, you can send them offline to ccb_at_bri.nrc.ca.)
>
> Regards,
>
> Enrico
>
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Alfredo Quevedo
> Sent: Tuesday, June 03, 2008 10:09 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Trajectory in "Sietraj"
>
>
> Dear Enrico: the error message is:
>
> (MarTetSurf: : Out3) MarTet_TMP_SIZE exceeded.
>
>
> Thanks
>
> Alfredo
>
>
>
> ----- Original Message -----
> From: "Purisima, Enrico" <Enrico.Purisima_at_cnrc-nrc.gc.ca>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, June 03, 2008 10:55 AM
> Subject: RE: AMBER: Trajectory in "Sietraj"
>
>
>> Dear Alfredo,
>>
>> The trajectory used is an Amber trajectory with water molecules
>> stripped
>> out and generated with the nobox option. The suffix .trj was an
>> arbitrarily chosen suffix in the examples and not meant to imply Gromacs
>> files. Could you post the error messages? A common cause of errors is
>> missing atom types.
>>
>> Regards,
>> Enrico
>> ---------
>> Enrico O. Purisima
>> Biotechnology Research Institute
>> National Research Council Canada
>>
>>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
>> Behalf
>> Of Alfredo Quevedo
>> Sent: Tuesday, June 03, 2008 9:35 AM
>> To: amber_at_scripps.edu
>> Subject: AMBER: Trajectory in "Sietraj"
>>
>>
>> Dear Amber users. I have recently seen the link of the "Sietraj"
>> application in Amberīs homepage, and found it ver interesting. I
>> downloaded it and run the examples with everything running ok. I tried to
>> apply this package to analyze my trajectories generated with Amber8 and
>> found some errors with the calculation stoped. Searching the source of
>> the
>> problem, I find out that the examples of Sietraj are based on a .trj
>> trajectory (I think that is Gromacs), so here comes my question: Has
>> anyone tryed this software using an Amber trajectory? Otherwise, is there
>> a way to convert the .mdcrd files into a .trj file?
>> Thanks in advance for the help,
>> Best regards
>>
>> Alfredo Quevedo
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