[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Wed Jul 23 18:12:11 CEST 2014
hello everyone
thank you justin but how can i increase the box size i am using the box
vector which is present in popc_whole.gro
how can i edit it
and one more problem when i see it in vmd my ligand is out side the protein
kindly help
On Wed, Jul 23, 2014 at 5:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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/
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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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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