[gmx-users] H-Db error

nikhil damle pdnikhil at yahoo.co.in
Mon Jul 20 11:49:20 CEST 2009

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 ?


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.

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