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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