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

[Pradip Kumar Biswas]

Hi,

My impression is that perhaps the error message is arising out of the
use of the old "top" folder from 3.2.1. For 3.3, the ffncadsnb.itp 
differs from 3.2.1
in that the 3.3 version contains and additional column for atomic 
numbers.
I encountered the same message while using OPLS but got it correct when
GMXLIB is correctly set to pick up the new "top" from 3.3.

cheers,
pradip.



On Oct 8, 2005, at 11:39 PM, Wang Zhun wrote:

> 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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>>>
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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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>
>
> _______________________________________________
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>
--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
"Big things in a Simpler way!!"
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