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

Justin Lemkul jalemkul at vt.edu
Wed Aug 13 16:20:37 CEST 2014 


On 8/13/14, 5:40 AM, neha bharti wrote:
> Hello Justin
>
> Thank you very much for your help.
>
> You have asked me that "Are the coordinates of lig.pdb identical to those
> of lig_princ_rotate.pdb?"
>
> The coordinates are not exactly the same. There is some variations. I have
> also check by some modifications in my steps like
>
> First I separate protein and ligand molecule (protein.pdb and ligand.pdb)
> and convert the ligand.pdb to ligand.mol2 as mention in SwissParam site.
>
> then generating pdb and itp file for ligand.mol2 (lig.pdb and lig.itp) from
> SwissParam then combine lig.pdb with protein file and then rotate it.
>
> But in this case also the coordinates of ligand.pdb and lig.pdb (file
> generated from SwissParam) is little bit different in decimal poins
>
> The following residues were different:
>
>
> ligand.pdb: 31 H032 lig A120      47.750   2.557  46.295  1.00  0.00
>
> SwissParam: 31 H032 LIG     1      47.750   2.558  46.295  1.00  0.00
>
>
> ligand.pdb: 35  H06 lig A120      50.798   8.692  47.839  1.00  0.00
>
> SwissParam: 35  H06 LIG     1      50.798   8.692  47.839  1.00  0.00
>
>
> ligand.pdb: 42 H133 lig A120      49.687   7.251  46.290  1.00  0.00
>
> SwissParam: 42 H133 LIG     1      49.688   7.251  46.290  1.00  0.00
>
>
> ligand.pdb: 45  H16 lig A120      47.131   3.806  48.240  1.00  0.00
>
> SwissParam: 45  H16 LIG     1      47.131   3.805  48.240  1.00  0.00
>
>
> ligand.pdb: 60 H261 lig A120      49.641   3.735  45.830  1.00  0.00
>
> SwissParam: 60 H261 LIG     1      49.641   3.735  45.831  1.00  0.00
>
>
> ligand.pdb: 61 H262 lig A120      50.356   5.354  46.021  1.00  0.00
>
> SwissParam: 61 H262 LIG     1      50.355   5.354  46.021  1.00  0.00
>
> Can I use this file??
>

The differences are insignificant and should not cause problems.

> I also did a change in --- editconf -rotate 0 0 90 to editconf -rotate 0 90
> 0
>
> because in when I rotate like -rotate 0 0 90 its parallel to lipid which
> was wrong.
>

It's not clear what your problem is from the description.  If you orient and 
position the protein-ligand complex in the box correctly, strip the ligand, and 
build the lipids around the protein, there should be no issue.  If you're still 
having problems, you'll need to post your files for download, at minimum some 
images that illustrate what's going on.

-Justin

>
> 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 ? 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
>
> ==================================================
>

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

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

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

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