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

[Justin Lemkul]

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

==================================================