[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 9 atomtypes or they might be negative.

[Justin Lemkul]

On Mon, Nov 25, 2013 at 4:53 AM, sunita gupta <sunita.bio at gmail.com> wrote:

> Hello everyone,
>
> I am trying to do implicit MD of protein-ligand complex using
> amberff99sb-ildn.
> I am getting following error at grompp minimization step
>
>  *GB parameter(s) missing or negative for atom type 'c3'GB parameter(s)
> missing or negative for atom type 'n2'GB parameter(s) missing or negative
> for atom type 'ce'GB parameter(s) missing or negative for atom type 'os'GB
> parameter(s) missing or negative for atom type 'cl'GB parameter(s) missing
> or negative for atom type 'h1'GB parameter(s) missing or negative for atom
> type 'hc'GB parameter(s) missing or negative for atom type 'ha'GB
> parameter(s) missing or negative for atom type
> 'hn'-------------------------------------------------------Program grompp,
> VERSION 4.5.5Source code file: grompp.c, line: 1123Fatal error:Can't do GB
> electrostatics; the implicit_genborn_params section of the forcefield is
> missing parameters for 9 atomtypes or they might be negative.For more
> information and tips for troubleshooting, please check the GROMACSwebsite
> at http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>*
>
> After reading earlier archive I tried -g disambguate option of acpype, but
> the atomtypes are still case sensitive. Also I tried to modify the
> gbsa.infile by adding these atomtypes with default vanderwalls radii
> and chaged
> two atomtypes in lig.itp by HA and N2 ( which is provided in gbsa.in), but
> the problem is still the same..
> GB parameter(s) missing or negative for atom type 'HA'
>
> GB parameter(s) missing or negative for atom type 'N2'
>
> GB parameter(s) missing or negative for atom type 'c3'
>
> GB parameter(s) missing or negative for atom type 'ce'
>
> GB parameter(s) missing or negative for atom type 'os'
>
> GB parameter(s) missing or negative for atom type 'cl'
>
> GB parameter(s) missing or negative for atom type 'h1'
>
> GB parameter(s) missing or negative for atom type 'hc'
>
> GB parameter(s) missing or negative for atom type 'hn'
>
> I don't understand why its again complaining about HA and N2, even if it is
> present in lig.itp.
>
>
Their presence in lig.itp is irrelevant; it's the fact that parameters are
not assigned for these atom types in gbsa.itp in the
[implicit_genborn_params] directive.

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
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


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