Set inp=1 and radiopt=0 in the &pb section. This error arises because the
non-polar solvation model has only parametrized some of the available atom
types in AMBER force fields (and none of the GLYCAM types, unless I'm
mistaken).
So the solution is to use the 'old' SASA-based method without dispersion
(inp=1) using the radii in the topology file instead of the optimized radii
(radiopt=0).
HTH,
Jason
On Mon, May 13, 2013 at 2:24 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear Amber users,
>
> I am trying to run MMPBSA for my complex (protein + peptide-sugar
> structure). My input file is:
>
> Sample input file for GB and PB calculation
> &general
> startframe=1, endframe=1000, interval=20,
> verbose=2, debug_printlevel=2, strip_mask=:WAT,Na+
> /
> &gb
> igb=2, saltcon=0.150,
> /
> &pb
> istrng=0.15, fillratio=4.0
> /
>
> MMPBSA_py command:
>
> MMPBSA.py -O -i mmpbsa_py.in -o MMPBSA_PB-GB.txt -sp COM_solvated.prmtop
> -cp COM.prmtop -rp REC.prmtop -lp LIG.prmtop -y *.mdcrd
>
> For prmtop files preparation I used GLYCAM_06h ff. During BFE calculations
> I am getting an error:
>
> File "/lap/amber/12.0.13/bin/MMPBSA.py", line 565, in <module>
> external_progs, '_MMPBSA_', normal_system)
> File "/afs/
> hpc2n.umu.se/lap/amber/12.0.13/amd64_ubuntu1004/bin/MMPBSA_mods/calculation.py",
> line 176, in run_calculations
> calc.Run()
> File "/afs/
> hpc2n.umu.se/lap/amber/12.0.13/amd64_ubuntu1004/bin/MMPBSA_mods/calculation.py",
> line 665, in Run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /lap/amber/12.0.13/bin/mmpbsa_py_energy failed with prmtop
> COM.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom 93 O1
> Os
>
> Exiting. All files have been retained.
>
> How could I avoid this error? Thank you in advance for your help.
>
> best regards
> /Urszula
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 13 2013 - 05:30:03 PDT
