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

[Erik Lindahl]

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