[gmx-users] required topology stuff modification for GBSA

[Mark Abraham]

On 06/24/2011 02:21 PM, Makoto Yoneya wrote:
> Dear GROMACS experts:
>
> I'd tried to use a GBSA implicit solvent function in ver. 4.5.4.
> I'd convinced the normal run with vacuo with simply high epsilon_r
> setting.
> After that, I'd modified the topology stuff by adding
> "[ implicit_genborn_params ]"
> entry and then
> implicit_solvent   = GBSA
> gb_algorithm       = OBC
> gb_epsilon_solvent = 78.3
> in the mdp file to try a GBSA implicit solvent run.
>
> Then I'd suffer error from grompp like as
> "Fatal error:
> Cannot find length for atoms 1-3 involved in angle".
>
> Actually, there is no covalent bond between 1-3
> (there is an angle with atoms 1-2-3, but these are
> bonded only with 1-2 and 2-3).

You don't say what your force field is, but those symptoms are 
suggestive of a problem with CHARMM force field lacking Urey-Bradley 
interaction parameters for atoms 1-2-3. If so, this is not a GB problem 
per se.

Mark

> I'm wondering what kinds of extra-modification in topology
> stuff besides adding "[ implicit_genborn_params ]" entry
> for the implicit solvent runs from the runs without it.
> Any info. will be welcome.
>
> Thank you for advance.
>
> Makoto Yoneya, Dr.
> AIST, Tsukuba
> JAPAN
> http://staff.aist.go.jp/makoto-yoneya/
>