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

[RINU KHATTRI]

hello gromacs users
i saw  in vmd system.gro its little bit ok very small fragment of protein
is out but in shrinkage.gro file box and protein is separated

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include ligand topology
#include "drag.itp"

; Include POPC chain topology
#include "popc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
  my topology file
kindly help
thanks in advance


On Wed, Jul 16, 2014 at 10:20 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> 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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>>
>>
>