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

[roshanak starlight]

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 ?

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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