[gmx-users] Protein ligand molecular dynamics simulation

sai nitin sainitin7 at gmail.com
Tue Apr 17 22:58:06 CEST 2012

Hi Justin,

I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand
topology using swissparam tool using Charmm force field  i included
ligand.itp file in topol.top of protein. And i used docked complex
structure (protein + ligand) from docking analysis and generated boxed.pdb
next i created solvated.pdb using (editconf and genbox tools) and  also
checked SOL molecules updated in topol.top file next i checked solvated.pdb
file in pymol  my ligand is in correct place in protein the way i wanted
but problem came after this while using grompp

I used grompp tool to minimize this solvated.pdb it is showing following
error..using em.mdp

Fatal Error
number of coordinates in coordinate file (solvated.pdb, 51540)
does not match topology (topol.top, 52756)

I know this is commonly known issue for new users of gromacs. I looked up
in gmx-archive list couldnt find optimal solution for my problem..

Let me know how to solve this ...issue...


On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> sai nitin wrote:
>> Hi all,
>> I have done complex (protein + ligand) complex from autodock software
>> using this complex im trying to follow
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>> gmx-tutorials/complex/01_**pdb2gmx.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html> tutorial
>> But when i take complex structure directly from autodock result and run
>> PDB2GMX it will give error because it is not recognizing ligand topology
>> which is in complex structure.
>> Then i followed justin tutorial took protein alone and applied Charmm27
>> Force field and used generate ligand topologies using Swissparam tool (
>> http://swissparam.ch/) when i do Editconf and created cubic box ligand
>> is going away from protein.
>> Actually my main task to place ligand in paraticular binding site in my
>> protein and perform molecular dynamics.
>> Can any body tell me how to do this..?
> Whatever you're doing is changing the coordinates that you originally had.
>  You don't want to do that.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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