AMBER Archive (2002)

Subject: Re: combinig two trajectory files.

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Mon Dec 02 2002 - 06:50:26 CST

Hi,

Try to use the NOBOX option in your carnal input file.
STREAM s1 md2.crd NOBOX

Cheers
pascal

Yongjun Jiang wrote:
>
> 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 

-- 
***************************************************
 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
 Manchester, M13 9PL, U.K
 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3