[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Anurag Dobhal]

Thank you Justin for your reply

as per your suggestion i verified the contents in confout.gro but i was
unable to check file as when i am clicking on it to open it I am getting an
message that file is of unknown type.

I again repeated the tutorial and I am getting the same things.

Thank you again for your time.

On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/30/14 5:51 AM, Anurag Dobhal wrote:
>
>> Hello gromacs users.
>>
>>
>> I am running GROMACS Tutorial of  KALP15 in DPPC.
>>
>> I am in the step define box and solvate.
>>
>> after the command
>>
>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
>> area_shrink1.dat
>>
>>
>> i am getting an error as
>>
>> Use of uninitialized value $box_x in multiplication (*) at
>> inflategro.pl line 339.
>> Use of uninitialized value $box_y in multiplication (*) at
>> inflategro.pl line 340.
>> Scaling lipids....
>> There are 0 lipids...
>> Illegal division by zero at inflategro.pl line 380.
>>
>> I am repeating the step third time and I am getting the same error.
>>
>> please help me how to skip this error.
>>
>>
> I suggested you verify the contents of confout.gro are sensible.  What did
> you learn?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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