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

[Justin Lemkul]

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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