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

[RINU KHATTRI]

hello gromacs users
i used vmd and both the command pbc box and periodic images in all 6 frames
+X -X +Y -Y +Z -Z and self but this action can not put protein inside the
box
and pbc box action only a box is created around protein and lipid 1/4
protein is in side the box
how to put it in side
kindly help


On Wed, Jul 16, 2014 at 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/16/14, 6:53 AM, RINU KHATTRI wrote:
>
>> hello gromacs users
>> i am working on protein complex with popc membrane
>> at the time of minimization and shrinking steps my protein complex is out
>> of the lipid membrane protein is in the lipid membrane till inflate.gro
>> but
>> after that it is out
>>
>
> This indicates that the protein is not properly centered or the box is of
> insufficient size to accommodate the components of the system.  Use "pbc
> box" in the Tcl console of VMD on the input and output structures and it
> should be obvious what is going on.
>
>
> -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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