[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for

[Mark Abraham]

On 2/06/2012 7:10 PM, xi zhao wrote:
> Dear gmx-users:
> When I try to simulation a system: protein + ligand molecule using the 
> Implicit Solvent method. the parameters of Ligand were produced by 
> acpype, but when grompped, the appeared"
> " Velocities were taken from a Maxwell distribution at 300 K
> GB parameter(s) missing or negative for atom type 'o'
> GB parameter(s) missing or negative for atom type 'os'
> GB parameter(s) missing or negative for atom type 'c'
> GB parameter(s) missing or negative for atom type 'c3'
> GB parameter(s) missing or negative for atom type 'hc'
> GB parameter(s) missing or negative for atom type 'h1'
> -------------------------------------------------------
> Program grompp_d, VERSION 4.5.3
> 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 6 atomtypes or they might be 
> negative."
> when I modified "4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>amber99sbr.ff/gbsa.itp 
> by adding the atomtype of ligand, the problem is still the same,
>

Then you apparently didn't add them correctly. See manual section 5.3.5 
and second paragraph of 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Mark
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