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

[Justin Lemkul]

On 5/19/14, 9:01 AM, Richard Smith wrote:
> Hi gmx-users,
>
> Is there ff12sb equivalent of gbsa_ff99sb.itp. Or an easy way to create one?
>
> Objective:
> 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 runs.
>
> 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
> problem.
>
> 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).
>

You can probably take reasonable values by analogy from existing files.  For all 
practical purposes, the contents of gbsa.itp are identical across all the Amber 
force fields.  Values of individual atomic radii vary very little between atom 
types, though there are a few functional group differences.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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