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

[Kyle Titus-Glover]

Sure, I can gather up the files and send them in a compressed folder to you
school email if that's ok.


Kyle Titus-Glover


On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:
>
>> 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?
>>
>>
> No, you should correct whatever it is that you're doing :)  InflateGRO
> can't un-delete lipids and it doesn't delete protein.  So you're issuing a
> command incorrectly, mismanaging files, or something else.
>
> As this is not actually a GROMACS problem, we can continue this off-list
> if needed.  I will need any relevant input and output files and an exact
> (copy-paste) of any commands used.  The tutorial works "out of the box," so
> there's something being mishandled if it's not.
>
> -Justin
>
>
> 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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>>>>
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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