AMBER Archive (2009)

Subject: Re: [AMBER] How to split mdcrd files

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Nov 15 2009 - 11:56:48 CST

sorry I misunderstood and thought you wanted to split it into protein
and dna. jason is right about using trajin/trajout. of course this
only shortens the traj file- if you were having problems in reading
the entire file it might not help. if it is just too many frames for
hbond analysis this will help.

another possibility is to not so hbond analysis on all frames by using
the stride setting in the trajin. using every tenth frame, for
example, may be just fine.

On 11/15/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> check the strip command- plenty of info in the archives and manual. it
> will do what you want.
>
> On 11/15/09, shamoon siddiqui <shamoonsiddiqui_at_gmail.com> wrote:
>> Dear All,
>> I am trying to do hydrogen bond analysis for my protein dna complex, but
>> the
>> problem is that my system is very big and my simulation is also of 20 ns.
>> That is why ptraj is giving segmentation error, i think because my mdcrd
>> file is too much heavy and when i did H-bond analysis with small mdcrd
>> file,
>> then suceed. So could anyone please tell me how to split mdcrd file into
>> several small mdcrd files, i think it is possible with ptraj, but i don't
>> know how to do. So please let me know in detail
>>
>> --
>> With best regards
>>
>> Dr. Shamoon Ahmad Siddiqui
>> DBT Postdoctoral Fellow
>> Molecular Biophysics Unit
>> Indian Institute of Science
>> Bangalore-560012, India
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Professor, Department of Chemistry
> CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
> ===================================================================
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================

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