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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
========================================
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