[gmx-users] OPLS implicit solvent problems

[Per Larsson]

Hi!

Thanks for pointing this out.
It is unfortunate that they are missing from the gbsa.itp-file. I will add them, but I do not have time today.
If you want to get going, you can add them yourself. 
The gb-parameters are essentially based on atom hybridization, so for each missing atom you find another that has the same (sp, sp2,sp3) hybridization, and add it to the gbsa.itp-file.

Cheers
/Per

21 jan 2011 kl. 13.51 skrev francesca.stanzione at unina.it:

> Hello,
> 
> I try to perform an implicit solvent simulation with Gromacs 4.5.3. version. I have a system corresponding to 6 peptides generated by Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the N-and C- termini as NH2 and COOH. My topology file is correct, and is all systems are included.
> 
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is included gbsa.itp
> 
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
> 
> ; Include water topology
> #include "./oplsaa.ff/tip3p.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>  
> ; Include topology for ions
> #include "./oplsaa.ff/ions.itp"
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> Protein_chain_C     1
> Protein_chain_D     1
> Protein_chain_E     1
> Protein_chain_F     1
> -----------------------------------------------------------------------------
> 
> When I start my simulations (md_start.mdp) in implicit solvent, i have this fatal error:
> 
> GB parameter(s) missing or negative for atom type 'opls_912B'
> 
> GB parameter(s) missing or negative for atom type 'opls_267'
> 
> GB parameter(s) missing or negative for atom type 'opls_269'
> 
> GB parameter(s) missing or negative for atom type 'opls_268'
> 
> GB parameter(s) missing or negative for atom type 'opls_270'
> 
> Program grompp, 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 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.
> 
> ----------------------------------------------------------------------------
> 
> Controlling these atoms they corresponding to:
> 
> opls_912B= the  CA of N-terminal residue
> 
> opls_267= Co in COOH
> 
> opls_268= Oh in COOH
> 
> opls_269= Oc in COOH neutral
> 
> opls_270= H in COOH
> 
> ----------------------------------------
> 
> in the file gbsa.itp in opls.ff directory these atoms missing. Now, have I done something wrong? If is all ok, is it possible to create these missing atoms in the gbsa.itp file?
> 
> thanx,
> 
> francesca stanzione
> 
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