[gmx-users] Problem with Lysozyme in Water Tutorial

[Justin Lemkul]

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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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================