[gmx-users] TIP3 water problem

[nikolaev at spbau.ru]

Hi, all!

I am working with the protein structure with internal waters of TIP3 type,
and running grompp ends with an error of "No default U-B types", as I
understand because of some internal inconsistency between atom types (H1,
H2 and OH2 in my tip3, HW1, HW2, OW in sol). I tried to rename atoms in
both topol.top and .gro files, add extra .itp file in charmm27.ff, nothing
worked.

However, this problem has already been mentioned here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087725.html

and the solution involved modifying top file (add waters information
manually). Is it really the only solution of this problem? Because as I
understand I need to insert manually all the charges, angles, bond lenths
for all the water molecules. And it seems quite a problem, if I want to
run more than 1 system.

Thank you in advance,
Dmitrii