[gmx-users] Genion cannot read from input

[Justin Lemkul]

On 4/27/13 12:28 PM, Justin Lemkul wrote:
>
>
> On 4/27/13 11:21 AM, Nathan Bullock wrote:
>> I am running genion neutralize the charge of my protein.
>> I got an error that wasn't very descriptive
>> Fatal error:
>> Cannot read from input
>> The part of the script that called this program read as follows
>> /usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p
>> protein_mod_filled5.top -o ions.tpr
>
> Was ions.tpr successfully generated?
>
>> /usr/local/gromacs-4.5.5/bin/genion -s ions.tpr -o solv_ions.pdb -p
>> protein_mod_filled5.top -pname NA -nname CL -nn 3
>> I am using the amber03 force field.
>> I had read on some of the pages that different forcefields used different
>> nomenclature for the ions used to neutralize the charge.
>>
>
> This is no longer true as of Gromacs 4.5, which has standardized nomenclature.
> You can always check ions.itp for your force field to be sure.
>
> The "cannot read from input error" only arises if (1) you are specifying a
> nonexistent index group (not applicable here) or (2) presumably if some input
> file does not exist.
>

Edit: the reason your script fails is that genion requires you to select a group 
for replacement.  You don't provide one, so it doesn't know what to read.  See 
the following:

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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