[gmx-users] Error in system_inflate.gro coordinates does not match

[RINU KHATTRI]

hello everyone
now i got the minimize structure after addition of water and ions (14 cl-)
i have been select  the

genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
-nname CL -nn 14

13 th option  sol  in out put

how can i analyze  my structure means is it ok or not because next
step is equilibration

kindly help



On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/11/14, 3:18 AM, RINU KHATTRI wrote:
>
>> hello
>> i am following the lysozyme tutorial
>>
>> editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0
>>
>
> Don't alter the box like this; it's totally nonsensical.
>
>
>    solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>
>>   but after running second command i got error  solvate command not found
>>
>> gmx solvate is also not working
>>
>>
> The tutorial corresponds to version 5.0; if you're using an older version,
> the command is called "genbox."
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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