[gmx-users] Implicit solvent calculatiom

[Mark Abraham]

On 16/06/2011 7:59 PM, Netaly Khazanov wrote:
> Hi,
> My system is protein +DNA.
> I am trying to perform implicit solvent calculation using Amber 99.
> In the begging I wanted to minimize the system and got this error message.
>
>
> GB parameter(s) missing or negative for atom type 'OS'
>
> GB parameter(s) missing or negative for atom type 'H2'
>
> GB parameter(s) missing or negative for atom type 'N*'
>
> GB parameter(s) missing or negative for atom type 'CM'
>
> GB parameter(s) missing or negative for atom type 'P'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: grompp.c, line: 1123
>
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the 
> forcefield is missing parameters for 5 atomtypes or they might be 
> negative.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> All the atoms, in which parametres are missing  belong to DNA.
> Should I add them manually to gbsa.itp? ( but i don't know the right 
> parameters?).

I expect you're going to have to check in the literature whether such 
parameters exist. Unfortunately, not every combination of everything can 
be available in a nice shrink-wrapped package :) Once you've found them, 
then you'll have to fill in the columns of the above-mentioned section 
accordingly.

Mark