[gmx-users] DPPC replication error

Priya Das priyadas001 at gmail.com
Thu Nov 27 09:28:12 CET 2014


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


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