[gmx-users] Bug/typo in ffG53a5/ffG53a6.rtp

[Berk Hess]

Hi,

I fixed it for 4.0.6 and 4.1.

Berk

> Date: Fri, 12 Jun 2009 14:19:32 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Bug/typo in ffG53a5/ffG53a6.rtp
> 
> 
> 
> Justin A. Lemkul wrote:
> > 
> > Hi all,
> > 
> > I have noticed that there is a problem with the NH2 directive in 
> > ffG53a5.rtp and ffG53a5.rtp.  The following lines are incorrect:
> > 
> 
> Edit: that should read "ffG53a5.rtp and ffG53a6.rtp"
> 
> -Justin
> 
> >  [ impropers ]
> >     -C -O N -CA gi_1
> >      N  H H  -C gi_1
> > 
> > They refer to the H atoms by type, not name.  They should instead read:
> > 
> >  [ impropers ]
> >     -C -O N -CA gi_1
> >      N  H1 H2  -C gi_1
> > 
> > If the user runs pdb2gmx on a structure containing NH2 they will get a 
> > fatal error:
> > 
> > "Atom H not found in residue 17 while adding improper"
> > 
> > I find that this typo has been present at least since version 3.3, and 
> > remains in version 4.0.5.
> > 
> > -Justin
> > 
> 
> -- 
> ========================================
> 
> 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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