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

sunita gupta sunita.bio at gmail.com
Tue Nov 26 13:47:20 CET 2013


---------- Forwarded message ----------
From: sunita gupta <sunita.bio at gmail.com>
Date: Mon, Nov 25, 2013 at 3:23 PM
Subject: Can't do GB electrostatics; the implicit_genborn_params section of
the forcefield is missing parameters for 9 atomtypes or they might be
negative.
To: gmx-users at gromacs.org


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.

Kindly guide in tackling this problem.
Thanks in advance

-- 
-- 
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio at gmail.com






-- 
-- 
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio at gmail.com


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