[gmx-users] Is there ff12sb equivalent of gbsa_ff99sb.itp?

Richard Smith res50 at cam.ac.uk
Mon May 19 15:01:09 CEST 2014

Hi gmx-users,

Is there ff12sb equivalent of gbsa_ff99sb.itp. Or an easy way to create 

To run an implicit solvent minimisation on 2yp7.pdb using the ff12sb 
force field.

Current Process is :
(1) Use amber12/bin/tleap to Amber inpcrd and prmtop files
(2) Use acpype to create GMX.gro and GMX.top files
(3) copy $PATH/gromacs/top/amber99sb.ff/gbsa.itp to current directory
(4) add "#include "./gbsa_ff99sb.itp" " to the .top file
(5) run a generic conjugate gradient minimisation. No ligands or ions 
are present

Running the same process ,but using the ff99sb force field the process 

With the ff12sb I get the below error message.

GB parameter(s) missing or negative for atom type 'CX'

GB parameter(s) missing or negative for atom type 'CO'

Program grompp, VERSION 4.6.5

I understand adding parameters for CX and CO to the .itp file will 
eliminate this

I am just unable:
to establish if any significant GBSA parameters have changed between 
ff99 and ff12
and if not
  where I can find the appropriate Gromacs parameters that should be 
used for
'CO' and 'CX' atom types ( and any other atom types used in ff1sb and 
not in ff99sb).


Richard Smith

Research Associate
Department of Zoology
Centre for Pathogen Evoluton
University of Cambridge
Downing Street
Cambridge CB2 3EJ

Tel.: +44 (0)1223 330933

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