[gmx-users] DPPC replication error

[Priya Das]

Dear Justin,

Sorry to bother you again and again.
I corrected the number of atoms in system1.gro. its completely fine.
Protein is centered in the 512 dppc bilayer with SOL.

But after inflation only 128 lipids are read; even though the protein is
centered.
..................
:   1  :   2    :
: ......*p*.........
: Lipid:     4  :
:..................
After inflate step, protein(*p)* is centered in the box but 1,2,4 are empty
and lipid marked portion is with 128 lipids.

please help

>
>
>
>> On Fri, Nov 21, 2014 at 8:07 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> 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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>>
>>
>>
>>
>>
>>


-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala