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

[Justin Lemkul]

On 7/23/14, 12:48 AM, RINU KHATTRI wrote:
> 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

Rendering the box vectors would be helpful, but my guess is your box is too 
small along z, so your protein jumps between periodic images, giving the 
impression that it is "outside" the membrane.

-Justin

> ; 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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>>>> Gromacs Users mailing list
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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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-- 
==================================================

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

==================================================