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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
