[gmx-users] DPPC replication error

[Justin Lemkul]

On 11/20/14 2:21 PM, Priya Das wrote:
> Dear Sir,
>
> The sequence of commands are as follows:
>
> # replicate 4 boxes of 128 dppc with SOL
> $ genconf -f dppc128.gro -o dppcnew.gro -box 2 2 1
>
> # generated .tpr file for new dppc with 512 lipid
> $ grompp -f minim.mdp -c dppcnew.gro -p topol_dppc.top -o em.tpr
>
> #removed periodicity
> $ trjconv -s em.tpr -f dppcnew.gro -o dppcnew_whole.gro -pbc mol -ur compact
>
> # inserted my protein in new lipid bilayer
> $editconf -f 1AKL.gro -o 1AKL_new.gro -c -box 12.41840 12.44350 6.59650
>
> #concatenate protein and lipid
> cat 1AKL.gro dppcnew_whole.gro > system.gro
>

Did you correctly update the second line of system.gro to reflect the actual 
number of atoms in the system?  This is the most likely source of error.

> #inflate.pl
>
> $ perl inflategro.pl system.gro 4 DPPC 0 system_inflated.gro 5 area.dat
>
> After running inflate.pl, the protein is centered in the empty box ;
> with only one quadrant filled with 128 lipid. the rest of quadrants
> are empty.
>

There should be no obvious quadrants here; the lipids should all be spread 
evenly throughout the expanded unit cell.  This observation suggests that my 
point above is correct; an incorrectly formatted .gro file has led to 
misinterpretation of the contents.

-Justin

-- 
==================================================

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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