[gmx-users] RE: Energy Minimization - not getting correct lipid area

Tue Jun 12 18:09:22 CEST 2012

Hi,

I am still working on this error but found that a possible error could be the way editconf was used to convert .pdb to .gro in Step 3. I used the command:

editconf -f dppc128.pdb -o dppc128.gro

Is this correct? Would it have been better to use pdb2gmx, instead? ( pdb2gmx –f input.pdb –o output.gro -o protein.top –inter ) Why use editconf?

Thanks!
________________________________
From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998249h38 at n6.nabble.com]
Sent: Friday, June 08, 2012 6:00 PM
To: Hicks, Erica
Subject: RE: Energy Minimization - not getting correct lipid area

On 6/8/12 6:54 PM, Erica Hicks wrote:
> How would I know what coordinate file to use? I have been following the
> tutorial word for word. However, I did not get the confout.gro file that I
> should have gotten after the minimization (mdrun -v -deffnm em) so I have
> been using em.gro. Would this be a problem?

No, confout.gro assumes you're using default names.  The em.gro file you
obtained is correct.  I have no idea how it's got 128 lipids in it though.
Check its contents.  If it has 128 lipids, you used an incorrect coordinate file
for grompp to prepare em.tpr.  That's about the only thing I can think that has
gone wrong.

-Justin

________________________________

> From: Justin A. Lemkul [via GROMACS]
> [[hidden email]<UrlBlockedError.aspx>] Sent: Friday, June 08, 2012 5:42 PM
> To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct lipid
> area
>
>
>
> On 6/8/12 6:33 PM, Erica Hicks wrote:
>
>> Hi,
>>
>> bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5
>> area.dat Reading..... Scaling lipids.... There are 128 lipids... with 50
>> atoms per lipid..
>>
>> Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
>> in the lower leaflet
>>
>> Centering protein.... Checking for overlap.... ...this might actually take
>> a while.... 100 % done... There are 2 lipids within cut-off range... 1 will
>> be removed from the upper leaflet... 1 will be removed from the lower
>> leaflet...
>>
>> Writing scaled bilayer&   centered protein...
>>
>>
>> Calculating Area per lipid... Protein X-min/max: 26    40 Protein
>> Y-min/max: 25    39 X-range: 14 A    Y-range: 14 A Building 14 X 14 2D grid
>> on protein coordinates... Calculating area occupied by protein.. full
>> TMD.. upper TMD.... lower TMD.... Area per protein: 2 nm^2 Area per lipid:
>> 10.4716089904762 nm^2
>>
>> Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet :
>> 10.4755772444444 nm^2
>>
>> Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet :
>> 10.4716089904762 nm^2
>>
>> Writing Area per lipid... Done!
>>
>> bash-3.2$ mdrun -v -deffnm em Back Off! I just backed up em.log to
>> ./#em.log.6# Getting Loaded... Reading file em.tpr, VERSION 4.5.4 (single
>> precision) Starting 4 threads Loaded with Money
>>
>> Making 1D domain decomposition 4 x 1 x 1
>>
>> Back Off! I just backed up em.trr to ./#em.trr.6#
>>
>> Back Off! I just backed up em.edr to ./#em.edr.6#
>>
>> Steepest Descents: Tolerance (Fmax)   =  1.00000e+03 Number of steps    =
>> 50000 Step=    0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03,
>> atom= 3275 Step=    1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax=
>> 2.40668e+03, atom= 3024 Step=    3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05
>> Fmax= 2.89119e+03, atom= 4225 Step=    5, Dmax= 3.6e-03 nm, Epot=
>> -3.12589e+05 Fmax= 1.46767e+03, atom= 1365 Step=    6, Dmax= 4.3e-03 nm,
>> Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365 Step=    7, Dmax= 5.2e-03
>> nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365 Step=    8, Dmax=
>> 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365 Step=    9,
>> Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365 Step=
>> 11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up em.gro to ./#em.gro.6#
>>
>> Steepest Descents converged to Fmax<   1000 in 12 steps Potential Energy  =
>> -3.1480012e+05 Maximum force     =  9.9022711e+02 on atom 1365 Norm of
>> force     =  1.2180042e+02
>>
>>
>> bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5
>> area_shrink1.dat Reading..... Scaling lipids.... There are 128 lipids...
>
> Something is wrong here.  You should only have 126 lipids since 2 were
> removed before.  Did you minimize the correct coordinate file?
>
>> with 50 atoms per lipid..
>>
>> Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
>> in the lower leaflet
>>
>> No protein coordinates found...
>
> This is also strange.  This, coupled with the lines above regarding the
> number of lipids, suggest you're using the wrong coordinate file.
>
>> Writing scaled bilayer&   centered protein...
>>
>>
>> Calculating Area per lipid... Protein X-min/max: 10000    -9999 Protein
>> Y-min/max: 10000    -9999 X-range: -19999 A    Y-range: -19999 A Building
>> -19999 X -19999 2D grid on protein coordinates... Calculating area occupied
>> by protein.. full TMD.. upper TMD.. lower TMD..
>
> The following areas are meaningless, for reasons associated with incorrect
> content or processing thereof.
>
>> Area per protein: 0 nm^2 Area per lipid: 0.583197761890625 nm^2
>>
>> Area per protein, upper half: 0 nm^2 Area per lipid, upper leaflet :
>> 0.583197761890625 nm^2
>>
>> Area per protein, lower half: 0 nm^2 Area per lipid, lower leaflet :
>> 0.583197761890625 nm^2
>>
>> Writing Area per lipid... Done!
>>
>> To me, it looks like it is not looking at the 126 lipids that I updated in
>> the topology file. Hmmmm....
>
> OK, I seem to remember 124 being what my system produced, but that's
> irrelevant. Check out the lines above.
>
>> Erica
>>
>> ________________________________ From: Justin A. Lemkul [via GROMACS]
>> [[hidden email]<UrlBlockedError.aspx>] Sent: Friday, June 08, 2012 5:21 PM
>> To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct
>> lipid area
>>
>>
>>
>> On 6/8/12 6:18 PM, Erica Hicks wrote:
>>> Hi,
>>>
>>> Everything should be updated correctly. I added in the DPPC 128
>>> underneath the protein in [molecules] but I still get the same results.
>>> What do you mean by " Further manual modifications are necessary based on
>>> how many lipids InflateGRO removes"? After I generated the new position
>>> restrain file, I updated the minim.mdp withe the correct info. I then
>>> scaled by a factor of 4, updated [molecules], ran energy minimization
>>> (mdrun -v -deffnm em), and
>>
>> This is all my comment meant.  If InflateGRO removes 4 lipids, then you
>> have 124 left, which it sounds like you have accounted for.
>>
>>> scaled by a factor 0.95. I have no idea what could possibly going wrong.
>>> Maybe something with the manipulation of InflateGRO????
>>
>> Please provide the entire screen output of the first shrinking step that
>> InflateGRO produces.
>>
>> -Justin
>>
>> -- ========================================
>>
>> Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
>> Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>
> -- ========================================
>
> Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
> Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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