[gmx-users] g_rms (was H-Db error)

[Justin A. Lemkul]

If you are changing the topic, please start a new thread to avoid confusion in 
the archive.

When running g_rms, you choose the group for analysis; there is no default.

-Justin

nikhil damle wrote:
> Hi,
> I want to know, by default g_rms calculates RMSD on which atoms set - 
> backbone, all atoms or c-alphas ? How do i modify these settings ?
> 
> Regards,
> Nikhil
> 
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Monday, 20 July, 2009 7:35:29 AM
> *Subject:* Re: [gmx-users] H-Db error
> 
> nikhil damle wrote:
>  > This is how i have modified the entry as i myself created the 
> parameter file for phosphothreonine. This is normal NH hydrogen n no 
> extra added=>directly copied from threonine. So y there is an error msg 
> ? i added this residue in aminoacids.dat file as well. and 2ns line is 
> tab separated. Is there any other formatting to b done ??
>  >
>  >
>  > TPO    1
>  > 1      1      H      N      -C      CA
>  >
>  >
>  >
>  > This is error msg i get: (I also checked h_db.c programme but could 
> not get much help abt the error msg)
>  > ---------------------------------------------------------------
>  > All occupancies are one
>  > Opening library file 
> /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp
>  > Atomtype 1
>  > Reading residue database... (ffG43a1)
>  > Opening library file 
> /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.rtp
>  > Residue 97
>  > Sorting it all out...
>  > Opening library file 
> /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb
>  >
>  > -------------------------------------------------------
>  > Program pdb2gmx, VERSION 4.0.5
>  > Source code file: h_db.c, line: 162
>  >
>  > Fatal error:
>  > Error reading from file ffG43a1
>  > 
> -------------------------------------------------------------------------------------------
> 
> That looks weird. Try spaces, not tabs. What does "pdb2gmx -debug 
> -yourflags" say? If you have an empty line at the end, try removing it.
> 
> Mark
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================