[gmx-users] KALP15 in DPPC
negar habibzadeh
negarhze at gmail.com
Mon Jan 15 16:56:33 CET 2018
tnx so much
i got nvt.tpr and now i want to run it but i am getting this error :
Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
I use position restraints on the lipid headgroups for P of DOPC . i add the
following lines to the system topology after the #include "dopc.itp" line.
#include "DOPC.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif
and i add the following line in nvt.mdp :
define = -DPOSRES_protein -DPOSRES_LIPID ; Position restraint
for each protein and for DOPC P
i created lipid_posre.itp :
; position restraint file for DOPC P
[ position_restraints ]
; i funct fcx fcy fcz
20 1 0 0 1000
~
i used position restraints for lipids but again when i want to run nvt ,i
get this error :
Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
how can i solve this problem ?
On Mon, Jan 15, 2018 at 6:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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