AMBER Archive (2002)

Subject: Re: combinig two trajectory files.

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Dec 02 2002 - 06:49:21 CST

if your prmtop file still has box info
(it is a periodic system) then you probably
do not want to use the "nobox" command in ptraj.
this will strip the box info, and that may be
what carnal is complaining about.
Carlos

----- Original Message -----
From: "Yongjun Jiang" <yjjiang_at_mail.shcnc.ac.cn>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, December 02, 2002 7:18 AM
Subject: combinig two trajectory files.

> Dear all,
>
> I have two trajectory files of molecular dynamics calculation. and I want
to analyse them
> together. Ptraj is used, ptraj script as following:
>
> ptrajin md0.crd
> ptrajin md1.crd
> ptrajout md2.crd nobox
>
> md2.crd was gotten. But I used carnal to measure RMSD, the error message
was shown:
>
> md2.crd : too many mumbers on box line for mdcrd format - bad coord file
or carnal bug.
>
> my input file of carnal.in :
> FILES_IN
> PARM p1 md.top ;
> STREAM s1 md2.crd ;
> FILES_OUT
> TABLE tab1 md_rms ;
> DECLARE
> GROUP gALL (RES 1-137);
> RMS r1 FIT gALL s1;
> OUTPUT
> TABLE tab1 r1;
> END
>
> How could I do? Thank you in advance.
>
>
>
>
> 　　　　　　　　　　　　　　Yongjun Jiang
> 　　　　　　　　　　　　　　yjjiang_at_mail.shcnc.ac.cn
> 　　　　　　　　　　　　　　　　　2002-12-02
>
>