[gmx-users] Protein ligand molecular dynamics simulation

[Mark Abraham]

On 18/04/2012 6:58 AM, sai nitin wrote:
> 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...

It means exactly what it says. Your coordinate file and topology must 
refer to the same system. See last para of manual 5.7.1.

Mark

>
> Cheers,
> Nitin
>
> On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>          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
>     MILES-IGERT Trainee
>     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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>
>
> -- 
>
> 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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