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

Fri Jul 15 15:55:35 CEST 2016

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

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
>>>
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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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