[gmx-users] GB parameter(s) missing or negative but they aint missing nor negative

[Justin Lemkul]

On 1/1/13 1:31 PM, Gert Peters wrote:
> Dear all,
>
> Im trying to run an md or em using an implicit solvation method using gromacs
> 4.5.5 but I allways get the same errors.
>
> GB parameter(s) missing or negative for atom type 'OS'
>
> GB parameter(s) missing or negative for atom type 'H2'
>
> GB parameter(s) missing or negative for atom type 'N*'
>
> GB parameter(s) missing or negative for atom type 'CK'
>
> GB parameter(s) missing or negative for atom type 'P'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> 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.
>
> Istart from default.pdb (41bp RNA) and perform following:
>
> pdb2gmx -f default.pdb -ff amber03 -water none -ignh
> editconf -f conf.gro -d 2 -bt triclinic -c
> grompp -f em_gbis.mdp -c out.gro
>
> with em_gbis.mdp containing:
>
> integrator= steep
> nsteps= -1
> nstlist= 10
> emstep=1
> rlist= 2.0
> coulombtype= cut-off
> rcoulomb= 2.0
> vdw-type= cut-off
> rvdw= 2.0
> nstenergy= 10
> implicit_solvent = GBSA
> constraints=none
> rgbradii=2.0
> gb_algorithm=OBC
> sa_algorithm=Ace-approximation
>
> Now the odd part is that I added all missing parameters to the
> /gromacs-4.5.5/share/top/amber...ff/gbsa.itp for example for H2:
>
> ...
> H4           0.1      1      1        0.115 0.85 ; H
> H5           0.1      1      1        0.125 0.85 ; H
> H2           0.1      1      1        0.125 0.85 ; H
> ...
>
> I tried doing this for amber 94, 99 and 03 but allways the same result.
>
> Anyone got a clue? I dont think I did something wrong as the implicit solvation
> model previously worked. All input is appreciated.
>

 From the path you've written above, it seems to imply you are modifying the 
gbsa.itp file in the source rather than the actual installed version.  Is that 
the case?  If so, are you editing it prior to installation?  That's the only way 
it will work, otherwise you need to make the changes in the amber03.ff 
subdirectory in $GMXLIB (/path/to/your/gromacs/share/gromacs/top).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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