[gmx-users] question about step 3 of kalp-15 in dppc
roshanak starlight
starlight.r77 at gmail.com
Fri Jul 15 21:16:13 CEST 2016
1.in end of topology file , i have sol.it dosen't water?should i remove
that?
2.minim.mdp file is not exist for this step
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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>>>>>>>>> or
>>>>>>>>> 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
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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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
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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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