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

[Justin A. Lemkul]

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).

> *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

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