[gmx-users] DPPC replication error

[Priya Das]

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

#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.




On Fri, Nov 21, 2014 at 12:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/20/14 11:53 AM, Priya Das wrote:
>
>> Dear All,
>>
>> I have replicated 128 DPPC lipid bilayer using genconf -box 2 2 1.
>> On viewing the structure in VMD i can find 512 lipid molecules. But after
>> inflate. pl step, i see my protein is centered in the box but there are
>> only 128 lipid molecules.
>> Please help
>>
>>
> It's impossible to help without your exact sequence of commands, start to
> finish.  There's no way for molecules to simply disappear.  Something had
> to have gone wrong along the way, but you haven't given us any relevant
> information to be able to say where.
>
> -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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-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala