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

Justin Lemkul jalemkul at vt.edu
Wed Feb 12 19:55:55 CET 2014

On 2/12/14, 12:33 PM, mabbasi wrote:
> dear all
> I am doing MD simulation of ligand-protein by GROMACS Tutorial for Drug –
> Enzyme Complex.
> I have done below steps:

 From the steps listed below, you are probably following some very old version 
of the tutorial by John Kerrigan.  He has updated the tutorial with a much 
better protocol, though it is similar in spirit.

> Use the Dundee PRODRG server to build a Gromacs89 topology for ligand.

FYI, it's GROMOS87, but the current version of PRODRG uses a newer GROMOS96 
parameter set, IIRC.

> 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.

You shouldn't be changing any numbers in pr.top, you should be altering the 
contents of trp.gro.  I strongly suspect this is your problem; what exactly did 
you do (copied and pasted from the terminal or actual files as needed, please).

> 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?

Removing waters won't solve your problem.  If the difference is 10, it's not 
anything to do with water.  Likely something went wrong when you pasted the 
ligand coordinates into trp.gro.  Either you did an incomplete paste, 
accidentally deleted some protein atoms, or did not update the number of 
coordinates on the second line correctly.



Justin A. Lemkul, Ph.D.
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


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