[gmx-users] missing gbsa parameters

Justin A. Lemkul jalemkul at vt.edu
Fri May 4 15:26:19 CEST 2012

On 5/4/12 9:14 AM, Vedat Durmaz wrote:
> thanks justin and alan.
> i also had the suspicion that the error is caused by case sensitivity. simply
> replacing all atom types from lower to upper case within the ligand.itp file
> yields the same error: "missing gb parameters".
> using the "--disambiguate" option for the parameterization with acpype has
> exactly no effect. the generated *_GMX.itp file still contains the same lower
> case letters for each atom type. am i doing something wrong?
> when using the "-atom amber" option (amber99sb instead of gaff), i do get upper
> case types, which are not always the same as given with "-a gaff". however,
> again, i am told by grompp, that GB parameters are missing for 15 atom types.
> and again, most of theese atom types ARE included in the respective gbsa.itp
> file (in share/gromacs/top/amber99sb.ff), but few are not.
> and according to those atom types that are not mentioned in grompp's error
> output: about half of them is listed in gbsa.itp while the other ones are not.
> i can't see any correlation between the atom types listed in my parameterized
> molecule's itp-file and the entries in gbsa.itp.
> does anyone have any idea? is there perhaps some other force field/database file
> that is checked apart from gbsa.itp?!

With respect to GB parameters, only gbsa.itp is checked; there is no auxiliary 
source of information.  If any atom type is not listed there, grompp will fail, 
as you're seeing.  For any missing atom type, you need to add appropriate 
parameters for it into gbsa.itp.  This may be trivial (redundancy in some atom 
types) or it may be difficult (deriving new parameters that are compatible with 
the parent force field).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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