[gmx-users] Number of coordinate in pr.top and solv.gro not matching

mabbasi mabbasi at pharm.mui.ac.ir
Wed Feb 12 19:33:40 CET 2014

dear all
I am doing MD simulation of ligand-protein by GROMACS Tutorial for Drug – 
Enzyme Complex. 

I have done below steps: 

Use the Dundee PRODRG server to build a Gromacs89 topology for ligand.
Rename the DRGGMX.ITP file to drg.itp (No errors in atom typing were found). 
Process the pr.pdb file with pdb2gmx(pdb2gmx -ignh -f pr.pdb -p pr.top -o 
pr.gro -missing -his) (53A6 force field) 
Copy and edit the coordinates from DRFIN.GRO onto the end of the trp.gro file.
Change the number at the pr.top file.
Add  #include “drg.itp”  after the forcefield parameter include statement in 
pr.top and Under the [ molecules ] section  add ligands name under Compound 
and 1 under #mols. 
Setup the box: 
editconf -bt dodecahedron -f pr.gro -o box.gro -c -d 1.2
genbox -cp center.gro -cs spc216.gro -o sol.gro -p pr.top
grompp -f em.mdp -c sol.gro -o ion.tpr -p pr.top

I am getting stuck at last command. Its showing following error:
Fatal error:
number of coordinates in coordinate file (sol.gro, 28814) does not match 
topology (pr.top, 28804)

I am looking forward to getting a reply from you on how to what leads to the 
error message.
What is it wrong in this process?
Different of between them is 10,and how can remove HOH of sol.gro file?

maryam abbasi, PhD student of Medicinal Chemistry
Department of Medicinal Chemistry,
Faculty of Pharmacy and Pharmaceutical Sciences (http;//pharm.mui.ac.ir/)
Isfahan University of Medical Sciences (http://www.mui.ac.ir), 
Hezar Jerib Ave. 

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