AMBER Archive (2004)

Subject: Re: AMBER: about mm_pbsa parameter

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Sep 24 2004 - 10:49:22 CDT

The first number in a snapshot crd file is the number of atoms.
You can also find it in the top region of the parmtop file (see
description of the amber file format:
http://amber.scripps.edu/formats.html#topo.cntrl -> NATOM is what you
are looking for)

Oliver

Xiao He wrote:
> In mm_pbsa
>
> a_at_MAKECRD
> #
> # The following parameters are passed to make_crd_hg, which extracts snapshots
> # from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 above.)
> #
> # BOX - "YES" means that periodic boundary conditions were used during MD
> # simulation and that box information has been printed in the
> # trajectory files; "NO" means opposite.
> # NTOTAL - Total number of atoms per snapshot printed in the trajectory file
> # (including water, ions, ...).
>
> I have no water in my top file ,how to determine the NTOTAL parameter?
>
>
> 　　　　　　　　Xiao He
> 　　　　　　　　hx_at_itcc.nju.edu.cn
> 　　　　　　　　　　2004-09-24
>
>
>
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-- 
________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke_at_u.washington.edu
________________________________________________________________

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