[gmx-users] Problem with Lysozyme in Water Tutorial

[Stephen P. Molnar]

On 02/03/2015 02:30 PM, Justin Lemkul wrote:
>
>
> On 2/3/15 2:16 PM, Stephen P. Molnar wrote:
>> Ok.  I understand the replys.
>>
>>   I only have a couple of further questions.
>>
>> A link to grompp is in /usr/local/gromacs/bin.
>>
>> Why isn't ions.mdp in the run directory and then, where is it?
>>
>
> You download it from the tutorial site.
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/04_ions.html 
>
>
> "An example .mdp file (the one we will use) can be downloaded here." 
> The word "here" is a clickable link to download the file.
>
> -Justin
>
>> Thanks in advance.
>>
>>
>> On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote:
>>> It just means you either missed grompp "-f ions.mdp" ...
>>>
>>> OR
>>>
>>> the ions.mdp file is not there in the directory where you are 
>>> performing
>>> your simulations.
>>>
>>> On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar 
>>> <s.molnar at sbcglobal.net>
>>> wrote:
>>>
>>>> I have installed v-5.0.4 in Debian Wheezy without any warning or erroe
>>>> messages.
>>>>
>>>> I have tried running the Lysozyme in Water Tutorial ( the one 
>>>> written for
>>>> v-5) and have generated an error message in Step 4.
>>>>
>>>> The message is:
>>>>
>>>> File input/output error:
>>>> ions.mdp
>>>> For more information and tips for troubleshooting, please check the 
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> I checked the reference and did not find one [defaults] directive 
>>>> in the
>>>> .itp file, let alone two
>>>>
>>>> Pleas advise.
>>>>
>>>> Thanks in advance.
>>>>
>>>> -- 
>>>> Stephen P. Molnar, Ph.D.                 Life is a fuzzy set
>>>> Foundation for Chemistry                 Stochastic and Multivariate
>>>> www.FoundationForChemistry.com
>>>> (614)312-7528(c)
>>>> Skype:  smolnar1
>>>>
>>>> -- 
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>>
>
Many thanks flr the reply.  It was my fault for not reading carefully 
enough.,

-- 
Stephen P. Molnar, Ph.D.                 Life is a fuzzy set
Foundation for Chemistry                 Stochastic and Multivariate
www.FoundationForChemistry.com
(614)312-7528(c)
Skype:  smolnar1