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

[RINU KHATTRI]

hello everyone
thank you justin
i did the same
till minimization without the ligand it is in the lipid and center but i
edit the box size arbitrary i used x and y axis as present in popc but in z
axis used 10.00000 so there is overlapping of protein and lipid  i think
this can create problem
help


On Wed, Jul 23, 2014 at 10:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/23/14, 12:12 PM, RINU KHATTRI wrote:
>
>> 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
>>
>
> editconf
>
>
>  and one more problem when i see it in vmd my ligand is out side the
>> protein
>>
>
> Position the protein-ligand complex like you want before packing the
> lipids around the protein, remove the ligand, then assemble the membrane
> protein system.  With strong restraints, the protein should not move, so
> you can just paste in the ligand coordinates afterwards.  Then adjust the
> box and solvate.
>
>
> -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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