[gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

should i do this ? :
 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and
system_inflated.gro from 6348 t0 6300 ?
but why is number of system.gro 6538 ? (6400 + 138)
50 is atom per lipid


On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/15/16 9:26 AM, roshanak starlight wrote:
>
>> hello . when i want to do energy minimizationin step 3 , with this
>>  command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
>> em.tpr
>>  (or confout.gro replace em.tpr) i face with this error:
>>
>> Fatal error:
>> number of coordinates in coordinate file (system_inflated.gro, 6438)
>>              does not match topology (topol.top, 138)
>>
>> Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC
>> 14
>> system_inflated.gro 5 area.dat
>> , i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of
>> this sentence in terminal:
>> There are 2 lipids within cut-off range...
>> 1 will be removed from the upper leaflet...
>> 1 will be removed from the lower leaflet...)
>>
>> where is the problem from ?
>>
>>
> Apparently you didn't actually update the topology.
>
> 126 * 50 = 6300
> 6438 - 138 = 6300
>
> So your topology specifies no lipids.
>
> -Justin
>
>
> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/15/16 4:56 AM, roshanak starlight wrote:
>>>
>>> excuse me i forgot that  write subject.
>>>>
>>>> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
>>>> starlight.r77 at gmail.com
>>>>
>>>> wrote:
>>>>>
>>>>>
>>>> hello
>>>>
>>>>> i use kalp-15 in dppc tutorial  that there is in this website :
>>>>> http://www.bevanlab.biochem.vt.edu
>>>>> i have 2 question about step 3 :
>>>>> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
>>>>> -fc 100000 100000 100000 which shoud i choose ?    ( i choose
>>>>> 1:protein .
>>>>> is it right ?)
>>>>>
>>>>>
>>>> From the tutorial:
>>>
>>> "The authors of the InflateGRO script recommend using a very strong
>>> position-restraining force on protein heavy atoms to ensure that the
>>> position of the protein does not change during EM."
>>>
>>> So choose the protein heavy atoms (Protein-H).
>>>
>>> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
>>>
>>>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
>>>>> thank you
>>>>>
>>>>>
>>>>> It doesn't matter.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> 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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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