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

[RINU KHATTRI]

hello everyone
ok justin iam sending you the link of images
http://s48.photobucket.com/user/mittukhattri/media/Screenshot-3_zps81b0c070.png.html
http://i48.photobucket.com/albums/f213/mittukhattri/Screenshot-3_zps81b0c070.png
; Include Position restraint file
#ifdef  POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "backbone_posre.itp"
#endif
; Include ligand topology
#include "drag.itp"

; Ligand position restraints
#ifdef   DPOSRES_LIG
#include "posre_UNK.itp"
#endif

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

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx          fcy         fcz
   1    1        1000000    1000000    1000000
   2    2       1000000    1000000    1000000
   3     3       1000000    1000000    1000000
#endif

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

[ system ]
; Name
Displayed atoms in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
UNK                 1
POPC               122
this is my topology
i will  add water and ions after the shrinking step
 i did't get inflategro2.pl script i used infltegro.pl
kindly help


On Tue, Jul 22, 2014 at 4:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/21/14, 11:30 AM, RINU KHATTRI wrote:
>
>> hello everyone
>>
>> thanks justin it works but problem is at the same place even one more
>> problem ligand is out side the protein and protein is out side the popc
>>
>
> So you've placed the ligand incorrectly or otherwise manipulated the
> coordinates wrong.  Given the absence of any other information, it's
> impossible to suggest anything.
>
> -Justin
>
>
>  kindly help
>>
>>
>> On Sat, Jul 19, 2014 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/19/14, 9:56 AM, RINU KHATTRI wrote:
>>>
>>>  hello everyone
>>>>
>>>> i know justin -D is for minim.mdp not for topology i used simply D
>>>>
>>>>
>>> That's still wrong.  There should be no "D" or "-D" in the #ifdef
>>> statement; it's cpp macro syntax.  Please look at the block I provided
>>> before:
>>>
>>>
>>> #ifdef STRONG_POSRES
>>> #include "strong_posre.itp"
>>> #endif
>>>
>>> Use it exactly.  Copy and paste it.  Invoke it with "define =
>>> -DSTRONG_POSRES"
>>>
>>>
>>> -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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> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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