[gmx-users] DPPC replication error

[Priya Das]

Dear Sir,

It worked.
The SOL molecules were the problem. I deleted the SOL molecules from
initial 128 DPPC pdb file and followed the rest steps.
Thankyou very much Sir.

On Thu, Nov 27, 2014 at 1:57 PM, Priya Das <priyadas001 at gmail.com> wrote:

> Dear Sir,
>
> Its still not working. The problem is wtih the .gro file.
>
> 3800DPPC    C31 8168   1.227   7.714   0.910  0.0000  0.0000  0.0000
>  3800DPPC    N41 8169   1.267   7.733   1.049  0.0000  0.0000  0.0000
>  3800DPPC    C51 8170   1.398   7.668   1.071  0.0000  0.0000  0.0000
>  3800DPPC    C61 8171   1.528   7.750   1.049  0.0000  0.0000  0.0000
>  3800DPPC    O71 8172   1.559   7.832   1.162  0.0000  0.0000  0.0000
>  3800DPPC    P818173   1.691   7.918   1.150  0.0000  0.0000  0.0000
>  3800DPPC    O918174   1.804   7.825   1.145  0.0000  0.0000  0.0000
>  3800DPPC   O1018175   1.675   8.017   1.039  0.0000  0.0000  0.0000
>  3800DPPC   O1118176   1.700   7.991   1.290  0.0000  0.0000  0.0000
>  3800DPPC   C1218177   1.586   8.043   1.360  0.0000  0.0000  0.0000
>  3800DPPC   C1318178   1.617   8.038   1.511  0.0000  0.0000  0.0000
>
> IF THERE IS NO SPACE BETWEEN THE ATOM NAME AND ITS NUMBER IT IS NOT READ.
> The lipid molecules are read when i manually insert space in .gro file.
>
> How do i tackle this problem.
>
> On Tue, Nov 25, 2014 at 6:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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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>
>
>
> --
> *Let us all join hands to save our " Mother Earth"*
> ------------------------------------------------------------------------
> Regards,
> Priya Das
> Research Scholar
> Dept. of Computational Biology and Bioinformatics,
> University of Kerala
>
>


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