[gmx-users] Itp file problem -- Atom type not found

Justin A. Lemkul jalemkul at vt.edu
Wed May 9 13:32:20 CEST 2012

On 5/9/12 3:13 AM, Sarath Kumar Baskaran wrote:
> Hi Justin,
> I had used only  Gromos 43 a1 from initially for proteins, but i saw the -ff gmx
> in the Drug enzyme tutorial, so i tried using this optiion for protein ligand
> comp[ex simultaitons, also the simulation was able to be performed with -ff gmx
> for some ligands without the atom type not found error. for all the ligands i
> used the itp (topology) file from PRODRG only

Depending on which version of PRODRG you used, this approach may or may not have 
been appropriate.  I'm assuming the tutorial you followed was John Kerrigan's, 
which is several years old and relies on an older version of PRODRG.  In any 
case, unmodified PRODRG parameters are insufficiently accurate for simulations, 
in every case that I have seen.  There are better tools available, and greater 
detail in parameterization is expected.  Interpret your results with care, and 
don't be shocked if reviewers of your papers do not believe the PRODRG results.

> I came accross the problem that u stated with PRODRG in the archives...
> Now for this protein ligand complex i am unable to used Gromos43a1, it says
> number of atoms mismatch
> but that problem of mismatch is due to the itp file included in the .top file
> For complexes i do add the .itp file in the .top file everytime during simulation...
> If in case the only way to solve this problem is to make manual improvements in
> the itp file....
> Can u please help me how to do the adjustments....I am sorry i dont know how to
> create a manual itp topology file...

Mismatch between coordinate and topology files is simply due to incorrect 
counting of molecules or failure to maintain a match between the two.  The 
solution is always the same - take greater care in bookkeeping throughout your 
workflow.  Any time the coordinate file is changed, so too must the topology. 
Some tools (genbox, genion) do this for you.  Anything else is up to you to 
verify and apply.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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