[gmx-users] error on version3.3-rc3

[Wang Zhun]

Hi,

Thank you for your help first.
The input structure was not wrong for Gromacs3.2.1 that I used before, and even the speptide demo can not work in order as for PDB2GMX version 3.3 rc3, so I think the problem lies in the rc3, or maybe the installation process.

Anyway I'll return to 3.2.1 to check the problem.

Thanks!

wzh

In your mail:
>From: Erik Lindahl <lindahl at sbc.su.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: leafyoung81-group at yahoo.com,
Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] error on version3.3-rc3
>Date:Sat, 8 Oct 2005 21:53:35 +0200
>
>Hi,
> 
> I can't repeat it either with my version-3-3-ready-but-not-yet- 
> released :-)
> 
> However, unless you have a specific reason it is probably better to  
> use OPLS rather than Encad.
> 
> Encad is pretty old, but has been optimized for very short cutoffs  
> and vacuum simulations. For general stuff OPLS-AA/L produces more  
> accurate results, as far as we know.
> 
> Cheers,
> 
> Erik
> 
> On Oct 8, 2005, at 8:00 PM, <leafyoung81-group at yahoo.com>  
> <leafyoung81-group at yahoo.com> wrote:
> 
> > --- Wang Zhun <wangzhun at pumc.edu.cn> wrote:
> >
> >
> >> Hi,
> >> I've installed version3.3-rc3.
> >> When I entered pdb2gmx, a prompt says:
> >> Opening library file
> >> /usr/local/gromacs/share/top/ffencads.hdb
> >> Opening library file
> >> /usr/local/gromacs/share/top/ffencads-n.tdb
> >> Fatal error: Reading Termini Database: expected 4
> >> items of atom data in stead of 3 on line
> >>                 M3      14.0067 -0.71
> >>
> > I couldn't reproduce your result. But my line in
> > ffencads-n.tdb reads as
> > N               M3      14.0067 -0.71
> >
> >> When I entered grompp, a prompt says:
> >> Fatal error: Bond atom type names can't be single
> >> digits.
> >>
> > To check why it is wrong, you can check yourselves.
> > Which line in your structure file has caused problem.
> >
> > I would like to encourage you to not only look at the
> > errors but look into why it is there. The information
> > given by gromacs is in quite a detail.
> >
> >> But editconf.genbox and mdrun all work properly.
> >> What are the differences between version3.2.1 which
> >> I used and version 3.3 and how should I solve these
> >> 2 problems?
> >> Thanks.
> >>
> >>
> >> _______________________________________________
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> >
> 
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
> 
> 
> 
> 
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