[gmx-users] GBSA implicit model and atom type

anna battistia at libero.it
Wed Jan 26 22:50:39 CET 2011

Dear all

I have got a problem with implicit water GBSA model.

My problem:

For my system I defined an atomtype in this way:
(I defined about 10 atoms type and for all I have got the same problem)

[ atomtypes ]
; name     bond_type  mass   charge ptype  sigma(nm)
NLAPT      NC         14.0067  0.314  A     0.29760      0.87672

if in the md.mdp file I set
implicit_solvent         = no

grompp tool give a good result, and mdrun can generate the good
but if I use the implicit solvent :   implicit_solvent         = GBSA

the tool grompp give the error:

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

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 8 atomtypes or they might be
For more information and tips for troubleshooting, please check the
website at http://www.gromacs.org/Documentation/Errors

so I put the following parameter in the gbsa.itp file the parameter:

[ implicit_genborn_params ]

; atype      sar      st     pi       gbr       hct
NLAPT         0.155    1      1.028    0.1488    0.79 ;  N

but grompp give the error

Couldn't find topology match for atomtype NLAPT

Can you give me an idea in order to solve this problem?
Thank you very much!!!


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