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

[RINU KHATTRI]

hello every one
i am working on complex with popc membrane after visualization of minimize
structure (after solvation and addition of ions 14 cl-) in VMD i saw
protein is moving out em.gro from the lipid membrane i dont know how to
resolve it

help


On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> 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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>
>