[gmx-users] Problem in Ligand-Protein complex in POPC

[Justin Lemkul]

On 8/12/14, 6:50 AM, neha bharti wrote:
> Thank you very much justin for your reply.
>
> But I am still facing the problem to include ligand in protein.
>
> Following step I am performing:
>
>
>   PDB file of  protein complex with ligand is taken from pdb
> then
>
> 1) editconf -princ -f protein.pdb -o protein_princ.pdb
>
> 2) editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb
>
>
> 3) separate protein and ligand files from protein_princ_rotate and then save
> then in different files
>
> protein file: protein_princ_rotate.pdb
>
> ligand file: lig_princ_rotate.pdb
>
>
>
> 4) generating pdb and itp file for small molecule
>    lig.pdb
>    lig.itp
>

Are the coordinates of lig.pdb identical to those of lig_princ_rotate.pdb?

>
> 5) Generation of topology files for protein:
>
> pdb2gmx -f protein_princ_rotate.pdb -water tip3p -ignh -o protein.pdb
> -nochargegrp
>
>
> 6) mearge protein.pdb and lig.pdb file in conf.pdb file
>
>
> 7) copy the files (mention in tutorial) from charmm36 force field and place
> them in new created folder charmm36_lipid.ff
>
>
> 8) Next, create a forcefield.doc file that contains a description of the
> force field parameters in it. Mine contains something like:
>
> CHARMM36 all-atom lipid force field (with CMAP), extended to include Berger
> lipid parameters
>

Don't do this!  CHARMM36 and Berger are incompatible.  CHARMM36 already includes 
the lipid force field.

>
> 9) changes in topology file "charmm36/tip3p.itp" to
> "charmm36_lipid.ff/tip3p.itp"
>
>
> 10) Add Ligand Topology file:
>
> ; Include ligand topology
> #include "lig.itp"
>
> ; Include water topology
> #include "charmm36.ff/spc.itp"
>

Don't use SPC.  It will re-define the water [moleculetype] and apply the wrong 
parameters.  Make sure you're using the CHARMM-specific TIP3P model (default in 
the charmm36.ff package we provide).  If you don't, the lipid force field will 
produce bad results.

> 11) The next adjustment to be made is in the [ molecules ] directive. To
> account for the fact that there is a new molecule in conf.gro, we have to
> add it here, like so:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> LIG                 1
>
> download the following files:
>
> popc128a.pdb - the structure of a 128-lipid POPC bilayer
> popc.itp - the moleculetype definition POPC
> lipid.itp - Berger lipid parameters
>

You need an all-atom model of the lipid bilayer.  CHARMM-GUI is a better source 
of these coordinates.  Don't use the united-atom Berger model from Peter 
Tieleman in this case.

>
> 12) Orient the protein and membrane
>
> Convert the popc128.pdb to .gro format with editconf and remove the initial
> periodicity.
>
> (a) Generate a .tpr file for a popc-only system using grompp.
>
> grompp -f em.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr
>
>
> (b) Use trjconv to remove periodicity:
>
> trjconv -s em.tpr -f popc128a.pdb -o popc_whole.gro -pbc mol -ur compact
>
> select 0 for system
>
>
> 13) orient the peptide within this same coordinate frame as lipid, and place
> the center of mass of the peptide at the center of this box:
>
> editconf -f conf.gro -o conf_newbox.gro -c -box 6.23910 6.17970 6.91950
>
>
> 14) Pack the lipids around the protein and ligand complex
>
> First, concatenate the protein and bilayer structure files:
>
> cat conf_newbox.gro popc_whole.gro > system.gro
>
>
> 15) Remove unnecessary lines
>
> 16) Now, generate this new position restraint file using genrestr and
> include it in topology file:
>
> genrestr -f conf_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>
> select 0 for system
>
> 17)In the .mdp file used for the minimizations, add a line "define =
> -DSTRONG_POSRES" to make use of these new position restraints.
>
>
> 18) seperate the ligand and protein file because InflateGRO not deal with
> small molecule.
>
> then InflateGRO script run:
>
> perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat
>
> 19) energy minimize:
>
> grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr
>
> mdrun -v -deffnm em
>
> another script command:
>
> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
>
> Another energy minimization step:
>
> grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr
>
> mdrun -v -deffnm em
> Repeat this step.
>
> area per lipid reached  ~69 Å square. Then I stop.
>
> then again include the small molecule to final system_shrink.gro file and
> after that I perform the steps that is given in tutorial.
>
>
>
> is this the right way. I am doing this because we have to show the
> interaction of ligand and protein. I first created the ligand protein
> complex and at the time of running inflategro.pl command I separate the
> ligand molecule and again include it after iterations of scaling down by
> 0.95.
>

In principle, yes - the ligand should be removed before running InflateGRO, then 
added once the system is properly compressed.  Have you detected some problem at 
this point?

> rest of the steps is same as given in tutorial.
>
>
>
> one more query can we use orientation of protein in membrane database
> http://opm.phar.umich.edu/
> for orientation of protein instead of editconf???
> as it is not giving me the correct alignment.
>

Never used it, so I can't comment.

-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

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