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

[Kyle Titus-Glover]

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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>