[gmx-users] DPPC replication error

[Justin Lemkul]

On 11/25/14 12:30 AM, Priya Das wrote:
> Dear Sir,
>
> I took 128 dppc.pdb, dppc.itp and lipid.itp from Tielemans site (
> http://people.ucalgary.ca/~tieleman/download.html). For my work i need to
> replicate 128 dppc.pdb four times to get 512 lipid molecules.
>
>
>
> 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
>

You need to remove periodicity effects before running genconf.

> # 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
>

This call to trjconv is not necessary, and periodicity should have been 
accounted for first.

> # 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
>

After doing this, you have to manually update the contents of the .gro file 
(removing intervening box vectors and title lines, updating the number of 
atoms); did you do this correctly?

-Justin

> #inflate.pl
>
> $ perl inflategro.pl system.gro 4 DPPC 0 system_inflated.gro 5 area.dat
>
> *After running inflate.pl <http://inflate.pl>, the protein is centered
> in the empty box ; with only  128 lipid. *
>
>

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

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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