[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Pawan Kumar wrote:
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I have used force constants of 100000 in position restraint .itp files 
>> for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
>> The mdp files are :
> 
> The .mdp files look reasonable enough, although I don't know why you are 
> applying position restraints during EM.  If it is for InflateGRO, that 
> is fine, but once the system is assembled, you should remove the 
> position restraints from the protein to minimize the system more.
> 
> And are you sure you want 300K?  DPPC will be in a gel phase at that 
> temperature.  If you want a more realistic fluid-phase model, you'll 
> have to go above 315K (323K is common).
> 

One thing I just noticed.  You don't have solvent in your position-restrained 
run?  That could be a big problem if the lipid headgroups are strongly repelled 
from one another.  Add solvent before doing anything other than EM.

-Justin

>> *Topology file :*
>> ; Include forcefield parameters
>> #include "ffoplsaa.itp"
>> #include "lipid.itp"
>> #include "dppc.itp"
>>
> 
> This section should not work, as written.  Have you modified lipid.itp 
> according to Chris Neale's half-epsilon double-pairlist method?  If not, 
> what you've done makes no sense.  The Berger lipid parameters 
> distributed through Tieleman's site are designed for use with the Gromos 
> force fields.  They can be modified (search in the archives), but that 
> can also be a source of error.  Users who have made mistakes in the 
> conversion have seen their systems explode.
> 
> -Justin
> 
>> ; Include chain topologies
>> #include "topol_A.itp"
>> #include "topol_B.itp"
>> #include "topol_C.itp"
>>
>> ;#ifdef POSRES
>> ;#include "lipid_posre.itp"
>> ;#endif
>>
>> ; Include water topology
>> #ifdef FLEX_SPC
>> #include "flexspc.itp"
>> #else
>> #include "spc.itp"
>> #endif
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>>
>> ; Include generic topology for ions
>> #include "ions.itp"
>>
>> [ system ]
>> ; Name
>> PROTEIN IN DPPC BILAYER
>>
>> [ molecules ]
>> ; Compound      #mols
>> Protein_A           1
>> Protein_B           1
>> Protein_C           1
>> DPPC              926
>> ;SOL             23552
>>
>> Please help with some suggestions.
>>
>> Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu 
>> <mailto:jalemkul at vt.edu>> wrote:
>>  
>>
>>     Pawan Kumar wrote:
>>
>>         Respected Sir,
>>
>>         Greetings from Pawan.
>>         I did the Inflategro procedure for the POPC bilayer generated
>>         using genconf.
>>         It took around 26 compressions for coming near the initial area
>>         (just above it).
>>         The minimization were all converged to Fmax < 1350.
>>         If I decrease the Fmax less than this I am getting machine
>>         precision.
>>         But when I proceeded with the final compressed structure for pr
>>         mdrun it gave lincs warnings and ended with segmentation fault.
>>         As an alternative to this bilayer I used the DPPC bilayer
>>         (pre-equilibrated) which is given in GMX-Benchmark distribution.
>>         I carried out the same steps of Inflategro. I used the cutoff of
>>         14 A in the inflation and compression step also.
>>         In this case the the Steepest Descents converged to Fmax < 1000
>>         in all the steps. The maximum force war never above 850.
>>         But when I did position restraint mdrun with the last compressed
>>         file I got Lincs warnings and Segementation fault after few
>>         steps (30 - 40 steps).
>>         Can you please help how to proceed ?
>>
>>
>>     If the minimization procedure is adequately finishing, then the
>>     problem comes from something you are doing.  If you post your .mdp
>>     file, we may be able to see if there are any obvious mistakes.
>>
>>     -Justin
>>
>>         Thanking you,
>>
>>         Yours sincerely,
>>         Pawan
>>
>>
>>         Justin A. Lemkul
>>         Graduate Research Assistant
>>         ICTAS Doctoral Scholar
>>         Department of Biochemistry
>>         Virginia Tech
>>         Blacksburg, VA
>>         jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
> 

-- 
========================================

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

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