AMBER Archive (2003)

Subject: Re: AMBER: question about ptraj?

From: rluo_at_uci.edu
Date: Thu Jul 24 2003 - 11:48:54 CDT

Hi Tom,

What's the citation for ptraj?

Best,
Ray

Thomas E. Cheatham, III wrote:
>
>
> What happens is that after the strip :1-968 (if this is done first)
> is that the residues are effectively renumbered so that now :969 is
> residue :1.
>
> What you show about should work, i.e. strip that higher numbered residues
> first.
>
> Alternatively,
>
> strip :1-968,970-976
>
> or
>
> strip ^:969
>
>
> Finally with the trajout command below you might want to add the
> "nobox" command to avoid writing box information to the trajectory.
>
>
> Good luck and let me know of further problems,
>
>
> \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> | Departments of Medicinal Chemistry and of University of Utah
> | Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
> | & Center for High Performance Computing Salt Lake City, Utah 84112
> |
> | e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
> \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418
>
>
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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
Department of Information and Computer Science
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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