[gmx-users] tip3p water model

dennis at iitk.ac.in dennis at iitk.ac.in
Thu Dec 2 21:19:41 CET 2004

hello gromacs users,
                    I am a new user of gromacs.I have a problem concerned with
usage of tip3p water model. I want to simulate my protein in water using tip3p
water model.

Here i found that my database ".top" file did not have the structure ".gro" file
for tip3p.So in order to generate the structure file,i took a box size of 2.0 nm
cubic dimension and filled water in it with a total system density of 990.94 Kg/m3.

But during the preprocessing of the input files for energy minimization,Ifound
that if I choosed "GROMOS96 43a1 force field"(during pdb2gmx usage),it gave me
an error
like this:

Generated 279 of the 1225 non-bonded parameter combinations
Cleaning up temporary file gromppa1i4Uk
Fatal error: Atomtype 'HW' not found!

But if i choose  "OPLS-AA/L all-atom force field" (during pdb2gmx usage),it
works fine and i get the procesed out file from grompp i.e ".tpr file"

Also if i choose  "OPLS-AA/L all-atom force field" and use SPC water,it works fine.

If i check the "pdb2gmx" help info, i find that "SPC" model is recommended for 
"GROMOS96 43a1 force field" while "TIP3P" along with "SPC" and other model is
recommended for other force filed.

Does this mean that I cannot use TIP3P model with "GROMOS96 43a1 force field"???

If that's not the case,what should I do to overcome this problem???

Also if "TIP3P" is meant only for "OPLS-AA/L all-atom force field",should i use
this force filed and simulate my protein?????
Please do shed some light into my queries.
                                             Thank you,
                                             Dilraj Lama

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