[gmx-users] can gromacs read amber trajectory

[David van der Spoel]

Lydia wrote:
>    I heard that previous version gomacs can read amber trajectory file 
> by changing name to .g87.  So I tried this command after renaming amber 
> trajectory to .87:
> 
>      g_gyrate -f nmwt.g87 -s nmwt.tpr -n index.ndx
>     
>      I got the following Segmentation fault error:
> ---------------------------------------------------------------------------------------------------
> :(abbreviated)
> Selected 1: 'Protein'
>  
>  Select File Format
> ---------------------------
> 1. XYZ File
> 2. XYZ File with Box
> 3. Gromos-87 Ascii Trajectory
> 4. Gromos-87 Ascii Trajectory with Box
>  
> Choice: 4
>  
> GROMOS! OH DEAR...
>  
> Number of atoms ? 17351
> Time between timeframes ? 1
>                                                                                 
> 
>  
> Reading frame     790 time  791.000
> Back Off! I just backed up gyrate.xvg to ./#gyrate.xvg.4#
> Segmentation fault
> --------------------------------------------------------------------------------------------------------
> 
>      Have someone had successful experience of using amber trajectory in 
> gromacs 3.3? Also  in trajectory, I have 800ps which means 800 sets of 
> coordinates and boxsize but it seems always read 790 sets (based on the 
> number of read frames prined out on screen).  If I try some other amber 
> trajectory with 100 sets, it seems to read to 90 sets only. Is it right? 
> Any suggestion is welcome..
> 
Are you sure you have a box in the trajectory?
GROMOS would only write the box when you have pressure coupling turned 
on but I don't know about Amber. Try option 3 anyway.
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++