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

roshanak starlight starlight.r77 at gmail.com
Fri Jul 15 18:15:58 CEST 2016


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 ?


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



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
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>
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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
>>>>> 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!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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