Re: RMS calculations

From: Pascal Bonnet <>
Date: Wed 21 Nov 2001 15:16:47 -0800

If you use correctly these programs you have to obtain the same result.
For example, these two input files have to give you the same result
(protein atoms are 1-200)

ptraj input file :
trajin ../md.trj.Z
trajout ./md.trj.out pdb dumpq
rms first mass out ptraj.out :1-200 nofit
strip :WAT

carnal input file :
 PARM p1 ../;
 STREAM s1 ../md.trj.Z;
 TABLE tab1;
 GROUP gALL (RES 1-200);
 RMS r1 FIT gALL s1;
 TABLE tab1 r1;

Explications in AMBER book:
ANAL is for the analysis of structure and especially molecular
mechanical energy of a single
configuration of a system. It can be run on structures both before and
after modification
by the energy programs. Running ANAL on the initial configuration of
your system is a
good way to locate errors in the structure that result in large
energies. Anal can also be
used for more sophisticated analyses of energy and structure.

CARNAL is a molecular dynamics analysis program. It is used for
geometrical measurements, root
mean square coordinate fitting, trajectory averaging, and other
structural analyses of MD
trajectories. CARNAL executes a programming language for filtering,
measuring and
comparing multiple streams of coordinate files (the language contains 44
keywords and
uses 10 punctuation/logical characters). As an example, one can use it
to build a trajec-
tory in which the solute is positioned for minimum root mean square fit
of residues in the
active site and only the first shell of waters is included.

PTRAJ is a general purpose utility that can examine and modify prmtop
files created by LEaP or
PARM. It can also process trajectory files created from MD simulations,
carrying out superpositions, extractions of coordinates, etc. Ptraj now
can compute correlation func-
tions, thus incorporating the capability of a variety of auxiliary
programs in earlier ver-
sion of Amber.

Nikolai Smolin wrote:
> Dear AMBER users,
> I used AMBER for simulation of proteins.
> And I want to calculate RMS (root mean square).
> I know that ptraj, anal and carnal can calculate RMS.
> But what programm better and what difference?
> Thanks in advance.
> Nikolai Smolin
> Physikalische Chemie I
> Universit?t Dortmund
> Otto-Hahn-Str. 6
> 44221 Dortmund
> Germany
> Fax: +49 / 231 / 755 3901
> E-mail:

Dr. Pascal Bonnet
School of Pharmacy and Pharmaceutical Sciences,
University of Manchester, Manchester, M13 9PL, U.K.
Tel:(+44) (0)161 275 2431
Received on Wed Nov 21 2001 - 15:16:47 PST
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