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

Justin Lemkul jalemkul at vt.edu
Fri Jul 15 22:25:30 CEST 2016 


On 7/15/16 3:16 PM, roshanak starlight wrote:
> 1.in end of topology file , i have sol.it dosen't water?should i remove
> that?
>

Again, topol_dppc.top has absolutely nothing to do with the topol.top that 
should be used for the protein-membrane system.  Ignore it once you have made 
the DPPC whole.  There is no water in the output configuration of InflateGRO, by 
design (the paper regarding this method explains why).  If you were to add 
water, you would have a half million atom system that would probably never 
minimize to anything sensible, as well as distorting your lipids.  Follow the 
tutorial exactly and do not confuse file names.

> 2.minim.mdp file is not exist for this step

Yes it does.  It is linked from the step 3 page.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/minim.mdp

-Justin

> On Jul 15, 2016 8:49 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/15/16 12:15 PM, roshanak starlight wrote:
>>
>>> thank you for answers
>>> after this command :grompp -f minim.mdp -c system_inflated.gro -p
>>> topol.top
>>> -o em.tpr
>>>  i receive 2 note :
>>>
>>> NOTE 1 [file topol.top, line 927]:
>>>   System has non-zero total charge: 4.000000
>>>   Total charge should normally be an integer.
>>>
>>> should i add ion ? with ion.itp  that is in gromos53a6_lipid.ff ?
>>>
>>>
>> No, because there is no water (nor should there be).
>>
>>
>>> NOTE 2 [file minim.mdp]:
>>>   The optimal PME mesh load for parallel simulations is below 0.5
>>>   and for highly parallel simulations between 0.25 and 0.33,
>>>   for higher performance, increase the cut-off and the PME grid spacing
>>>
>>> .what is it's reason and what should i do ?.i used from same minim.mdp
>>> file
>>> that was for dppc( in tutorial.)
>>> should i change cut off ?on what basis? i don't find it in manual
>>>
>>>
>> Use the files from the tutorial.  Performance during EM is not anything of
>> major importance.  There's no way to take a huge, inflated system in vacuo
>> and make it very efficient.
>>
>> -Justin
>>
>>
>>>
>>> On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/15/16 9:55 AM, roshanak starlight wrote:
>>>>
>>>> excuse me.i don't understand .  should i update [molecule]  just  in
>>>>> *topol.top* ? how?
>>>>> my topol.top file in [molecule] has not any number :
>>>>>
>>>>> [ molecules ]
>>>>> ; Compound        #mols
>>>>> Protein             1
>>>>>
>>>>>
>>>>> Add a line that says "DPPC 126"
>>>>
>>>> You have to manually account for changes that are being made to the
>>>> coordinate file.  Please do some more basic tutorial material if the
>>>> content and organization of a topology is unfamiliar to you.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> in my topol_dppc.top is this:
>>>>
>>>>>
>>>>> [ molecules ]
>>>>> ; molecule name nr.
>>>>> DPPC 128
>>>>> SOL 3655
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 7/15/16 9:40 AM, roshanak starlight wrote:
>>>>>>
>>>>>> should i do this ? :
>>>>>>
>>>>>>>  i should change dppc from  128lipid (topol_dppc.top) to 6300atom and
>>>>>>>
>>>>>>>
>>>>>>> topol_dppc.top is only ever used for making molecules whole, and never
>>>>>> again.
>>>>>>
>>>>>> system_inflated.gro from 6348 t0 6300 ?
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Do not change the .gro file at all.
>>>>>>
>>>>>> but why is number of system.gro 6538 ? (6400 + 138)
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> In system.gro (and the corresponding topol.top) you have 128 lipids
>>>>>> and
>>>>>> the peptide.  Then InflateGRO removes two of those lipids, so you have
>>>>>> to
>>>>>> account for this in topol.top, which now has the peptide and 126
>>>>>> lipids.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
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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
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>> posting!
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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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
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>>>>>>
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
>>
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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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