[gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?

On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover <kyle136 at vt.edu> wrote:

> I tried restarting the whole process to go back and carefully look and
> make sure that nothing was spelled right. Bu I still get the same error.
>
>
> On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:
>>
>>> Hey everyone,
>>>
>>> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
>>> to get past 2. packing the lipids around the protein and 3. solvating
>>> with
>>> water. The follow the instructions step by step but for some reason as I
>>> try to run EM  with
>>>
>>> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp
>>>
>>> I get hit with this error:
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (system_shrink1.gro, 6400)
>>>              does not match topology (topol.top, 6438)
>>>
>>>
>> 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =
>> 6400) so something has gone badly wrong here.  Your coordinate file at this
>> point should have the peptide and 126 lipids; the InflateGRO output below
>> looks correct. Check the contents of system_shrink1.gro and make sure you
>> haven't perhaps accidentally renamed a file something that it shouldn't be.
>>
>> -Justin
>>
>> I figured that since my number of molecules were off that the problem was
>>> either the way I updated the molecules section of my topol.top fill by
>>> adding
>>> DPPC               126
>>>
>>> after seeing this when adding lipids:
>>>
>>> There are 128 lipids...
>>> with 50 atoms per lipid..
>>>
>>> Determining upper and lower leaflet...
>>> 64 lipids in the upper...
>>> 64 lipids in the lower leaflet
>>>
>>> Centering protein....
>>> Checking for overlap....
>>> ...this might actually take a while....
>>> 100 % done...
>>> There are 2 lipids within cut-off range...
>>> 1 will be removed from the upper leaflet...
>>> 1 will be removed from the lower leaflet...
>>>
>>> But for some reason I can't seem to start the EM iterations because of
>>> this
>>> error.
>>>
>>> Sincerely,
>>>
>>> Kyle Titus-Glover
>>> Virginia Tech '17 | Engineering Science & Mechanics
>>> Dean's Research Assistant, College of Engineering
>>> 443-802-4058
>>>
>>>
>> --
>> ==================================================
>>
>> 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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>
>