Atomtype OWT3 not found

I don't know how you are trying to use TIP3P water model. You can specify your water model using "pdb2gmx -water tip3p" or you can mannualy add " #include "tip3p.itp" " to you topology file. But in case of adding water you have to use -- "genbox -cs spc216.gro ........". This (http://gromacs.5086.x6.nabble.com/water-models-tip3p-gro-and-spce-gro-td5006864.html) link may help.

Felix Rausch

You do not have to change any force field files to fix this problem! If you used pdb2gmx to build your topology file and chosed tip3p as water model, everything should be fine.

Check your topology .top file. It should contain a line like this:

#include "gromos53a6.ff/tip3p.itp"

which loads the tip3p descriptions from the force field folder.

Juganta K Roy

Thanks for the replies. Dear, I got this error message after including "gromos53a6.ff/tip3p.itp" and also I added OWT3 and HW at the bottom of the .atp file and also corrected nonbonded.itp file of the corresponding force field.

Is there any suggestion?

Ricardo J Ferreira

Hello.

So you didn't created a new file from pdb2gmx? Then, the problem must be in your .gro file, where water is defined as OW and H (spc) and not TIP3P. You must change the atom naming within the GRO file in order to use the tip3p.itp.

Ricardo

Felix Rausch

Could you show us your .top and maybe also .gro file? Something seems to go wrong there, but it is difficult to give suggestions "out of the dark".

Ricardo J Ferreira

Hello

Exactly, you have SOL with SPC atoms.

79SOL OW 1681 0.307 0.213 1.231

79SOL HW1 1682 0.284 0.250 1.321

79SOL HW2 1683 0.277 0.118 1.225

OW, HW1 and HW2 is from SPC water. You have to change OW to OWT3 and HW1/HW2 to HW to assume TIP3P water!

Ricardo

Juganta K Roy

Thanks Ricardo. I tried with this but it shows the same error. As far I know OWT3 is atomtype and OW is atom name. Atom names are same for all water model.

Ricardo J Ferreira

Juganta,

you are right. Foolish me to mix atomtype with atomname... dah!

Nonetheless, I've tried and gave me the same error. This means that GROMOS forcefield in GROMACS isn't capable of using TIP3P because, in ffnonbonded.itp, there isn't any OWT3 atomtype.

You can add it, of course, but is never a good idea to mix/change/alter forcefields if you are planning to publish your work later on.

In GROMACS, the only FF that have TIP3P are GMX, GROMOS43A1 and OPLS. This information is given by /opt/gromacs-4.6.3/share/gromacs/top/tip3p.itp:

; This file is for backward compatibility only.

; Please directly include the tip3p.itp file from your force field directory.

#ifdef _FF_GROMACS

#include "gmx.ff/tip3p.itp"

#endif

#ifdef _FF_GROMOS96

#include "gromos43a1.ff/tip3p.itp"

#endif

#ifdef _FF_OPLS

#include "oplsaa.ff/tip3p.itp"

#endif

Hope it helps this time!

Ricardo

Juganta K Roy

Ok, Ricardo. If I want to use 43a1 force field in stead of 53a6, what should I do? Can I use the same topolgy, structure and itp files in case of 43a1 force field?

Really I appreciate your help.

Daniel Madulu Shadrack

Dear All,

I am doing Protein-Ligand interaction using gromacs, I am equilibrating the system by NVT using this command

gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

but I am getting an error below

Fatal error:

Atomtype CH1 not found

Help, what could be my mistake

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