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

[Justin Lemkul]

On 6/20/16 4:08 PM, Kyle Titus-Glover wrote:
> Sure, I can gather up the files and send them in a compressed folder to you
> school email if that's ok.
>

Yes.  The sequence of commands (in an executable script) is also essential.  A 
dump of files is only a small part of the equation.

-Justin

>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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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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-- 
==================================================

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

==================================================