AMBER Archive (2009)

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

From: Carlos Simmerling (
Date: Sun Nov 15 2009 - 11:28:06 CST

check the strip command- plenty of info in the archives and manual. it
will do what you want.

On 11/15/09, shamoon siddiqui <> 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

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:
Stony Brook, NY 11794-5115 Web:

_______________________________________________ AMBER mailing list