[gmx-users] build membrane system from Charmm-Gui

[Xiang Ning]

Dear Justin,

Thanks a lot! I am looking forward to the new version CHARMM-GUI. However, at this moment, I was trying to put a protein inside the membrane. I used "editconf -f protein.pdb -o conf.pdb -box (my box demension x y z)" and then "genbox -cp conf.pdb -cs lipid_water_ion.pdb -o box.pdb" to remove the overlapped lipids. It looks fine in VWD, no overlap between protein and lipids occurred. However, when I try to generate top file by using " pdb2gmx -f box.gro -p box.top", It showed it did not know "K" (potassium). So I change all "K" to origin Charmm version "POT" in box.gro file, it can generate top file this time, but when I ran "grompp -f minim.mdp -c box.gro -p box.top -o box.tpr", it showed "Unknown cmap torsion between atoms 319 321 323 338 341".  I downloaded the patch "0001-Fix-pdb2gmx-merge-cmap.patch" to fix the problem, but it did not work (it asked file to patch which I don't know which file to patch). I would like to know, how to ran energy
 minimization in this case (protein inside the lipid membrane)? I used charmm36 force field for all atom by the way.

Thanks very much for your patience and assistance!

Best,
Ning


On Sunday, August 24, 2014 4:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 8/24/14, 4:36 PM, Xiang Ning wrote:
> Dear Justin,
>
>
>
>
>
> Thanks for your help! It did work when I use grompp to generate tpr file.
> However, after obtaining  em.tpr file, I want energy minimization of the
> membrane+water+ion system, so I typed "mdrun -v -deffnm em", and the outcome
> em.gro file looks really weird by using VMD to view. The original file is
> water above the lipid membrane, but now by viewing em.gro, the water is now
> in the middle of two membrane leaflet, and they aparted to 4 parts! I would
> like to know what is wrong? Is it because the mdp file? Thanks very much for
> your assistance!
>

This is just a difference in convention.  CHARMM builds unit cells centered at 
the coordinate origin.  Gromacs centers at (x/2, y/2, z/2), so the molecule get 
re-wrapped due to PBC.  Re-centering the system within the box with editconf 
prior to anything else will fix the issue.

FYI We are working on a new version of CHARMM-GUI that will interface seamlessly 
with Gromacs.  It will be available soon.


-Justin

> Best, Ning
>
> my mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ;
> Parameters describing what to do, when to stop and what to save integrator
> = steep         ; Algorithm (steep = steepest descent minimization) emtol
> = 1000.0        ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm emstep      = 0.01      ; Energy step size nsteps          = 50000
> ; Maximum number of (minimization) steps to perform ; Parameters describing
> how to find the neighbors of each atom and how to calculate the interactions
> nstlist         = 1                 ; Frequency to update the neighbor list
> and long range forces ns_type         = grid          ; Method to determine
> neighbor list (simple, grid) rlist           = 1.2           ; Cut-off for
> making neighbor list (short range forces) coulombtype     = PME           ;
> Treatment of long range electrostatic interactions rcoulomb        = 1.2
> ; Short-range electrostatic cut-off rvdw            = 1.2           ;
> Short-range Van der Waals cut-off pbc                 = xyz               ;
> Periodic Boundary Conditions
>
>
>
> On Friday, August 22, 2014 4:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
>
>
> On 8/22/14, 4:36 PM, Xiang Ning wrote:
>> Hi All,
>>
>> I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions
>> and water from CHARMMGUI pdb and save just the membrane pdb, and use this
>> pdb with pdb2gmx to get top file (I used charmm36), then I would like to
>> know, how to add water and ions back to the system? I read the previous
>> solution was to modify [molecules] in top file (add ions and waters
>> information manually), are there any detailed explanation of how to do
>> that?
>>
>
> For the coordinates, just paste the water and ion coordinates back into the
> membrane-only file.  For the topology, indeed all you need to do is modify
> [molecules] in the .top to reflect however many waters and ions there are in
> the reconstructed system.
>
> -Justin
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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