[gmx-users] DPPC replication error

[Justin Lemkul]

On 11/21/14 3:26 AM, Priya Das wrote:
> 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
>

Upload the input coordinate file somewhere it can be downloaded.  Provide a URL 
for the download so that anyone else who wants to help can have a look.

-Justin

>>
>>
>>
>>> 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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>>>
>>>
>>>
>>>
>>>
>>>
>
>

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

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

==================================================