[gmx-users] KALP15 in DPPC

Mon Jan 15 15:59:39 CET 2018

On 1/15/18 6:18 AM, negar habibzadeh wrote:
> 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?

The error specifies that you've got "D0PC" instead of "DOPC" somewhere 
in the .mdp file (note zero instead of the letter O).

-Justin

>
> 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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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