[gmx-users] KALP15 in DPPC

Mon Jan 15 12:18:26 CET 2018

tnx Justin .
now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
your tutorial, in NVT equilibration step I created index file , with
program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
  0 System              : 30700 atoms
  1 Other               : 18744 atoms
  2 FR1                 :   160 atoms
  3 FR2                 :   220 atoms
  4 FR3                 :   240 atoms
  5 FR4                 :   205 atoms
  6 FR5                 :   255 atoms
  7 DOPC                : 17664 atoms
  8 CL                  :    40 atoms
  9 Water               : 11916 atoms
 10 SOL                 : 11916 atoms
 11 non-Water           : 18784 atoms
 12 Ion                 :    40 atoms
 13 FR1                 :   160 atoms
 14 FR2                 :   220 atoms
 15 FR3                 :   240 atoms
 16 FR4                 :   205 atoms
 17 FR5                 :   255 atoms
 18 DOPC                : 17664 atoms
 19 CL                  :    40 atoms
 20 Water_and_ions      : 11956 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
 'ri': residue index

> 2|3|4|5|6

Copied index group 2 'FR1'
Copied index group 3 'FR2'
Merged two groups with OR: 160 220 -> 380
Copied index group 4 'FR3'
Merged two groups with OR: 380 240 -> 620
Copied index group 5 'FR4'
Merged two groups with OR: 620 205 -> 825
Copied index group 6 'FR5'
Merged two groups with OR: 825 255 -> 1080

 21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms

> name 21 protein

> 21|7

Copied index group 21 'protein'
Copied index group 7 'DOPC'
Merged two groups with OR: 1080 17664 -> 18744

 22 protein_DOPC        : 18744 atoms

> 10|8

Copied index group 10 'SOL'
Copied index group 8 'CL'
Merged two groups with OR: 11916 40 -> 11956

 23 SOL_CL              : 11956 atoms

> q

then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)  I'm getting this error:
Fatal error:
Group D0PC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

my nvt.mdp file is that

Can anyone help me with the following fault in Gromacs during the NVT
equilibrium?

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/7/18 3:07 AM, negar habibzadeh wrote:
>
>> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
>> your tutorial  When I use inflategro script For my System I have got
>> Output System_inflated.gro file with certain message in Command prompt
>> as follows  . The Below Message Shows That There is No Lipid Molecules
>> Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
>> the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
>> Molecules Need to be Deleted ?
>>
>
> Maybe there just aren't any lipids overlapping with the protein; that can
> happen.
>
> -Justin
>
>
> There are 128 lipids...
>> with 138 atoms per lipid..
>>
>> Determining upper and lower leaflet...
>> 64 lipids in the upper...
>> 64 lipids in the lower leaflet
>>
>> Centering protein....
>> Checking for overlap....
>> ...this might actually take a while....
>> 100 % done...
>> There are 0 lipids within cut-off range...
>> 0 will be removed from the upper leaflet...
>> 0 will be removed from the lower leaflet...
>>
>> Writing scaled bilayer & centered protein...
>>
>>
>> Calculating Area per lipid...
>> Protein X-min/max: 24    41
>> Protein Y-min/max: 23    43
>> X-range: 17 A    Y-range: 20 A
>> Building 17 X 20 2D grid on protein coordinates...
>> Calculating area occupied by protein..
>> full TMD..
>> upper TMD....
>> lower TMD....
>> Area per protein: 3.25 nm^2
>> Area per lipid: 10.7582741393 nm^2
>>
>> Area per protein, upper half: 2.25 nm^2
>> Area per lipid, upper leaflet : 10.7738991393 nm^2
>>
>> Area per protein, lower half: 2.5 nm^2
>> Area per lipid, lower leaflet : 10.7699928893 nm^2
>>
>> Writing Area per lipid...
>> Done!
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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