[gmx-users] Centring a protein complex

[Rohit Farmer]

Hi Justin,

Thanks for the advice. It was the problem with the .xtc file I was using it
worked when I used the .trr file I think something went wrong while
downloading the files from our computer cluster.

One more qustion I have. My molecule looks broken at several places. I know
that it is just an artefact and not that its actually broken. But is there
a way to make then look whole. I tried the option whole with -pbc but
couldn't figure out what it actually did.

Thanks

Rohit

On Wed, Oct 29, 2014 at 12:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/29/14 8:08 AM, Rohit Farmer wrote:
>
>> Hi Guys,
>>
>> I am trying to centre a protein complex using this command
>>
>> trjconv -pbc mol -center -ur compact -s em.tpr -f md_0.xtc -o
>> md_0_center.xtc
>>
>> I selected "protein" in the first option and then "system" in the second
>> for output but I received the following error
>>
>> Floating point exception1900.000        ->  frame   3000 time
>> 30000.000
>>
>> I read somewhere that while centring a protein complex its better to
>> select
>> one monomer than the whole protein complex. So I tried doing that as well
>> by making an index file but I still received the same error. Can someone
>> please help me with this.
>>
>>
> The floating point exception would suggest that the trajectory is
> corrupted. What does gmxcheck tell you?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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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