Hi,
Note that if you use radiopt=0, you get an incorrect dispersion term, as
I reported before:
http://archive.ambermd.org/201906/0179.html
Thomas Gaillard
Le Tuesday 06 August 2019 à 09:50:54PM, rluo.uci.edu a écrit :
> Jeyaram,
> If you're using an older version, such as amber 16, please add radiopt=0 in
> your PB keyword section of the input file.
> But please update to the latest version ... it's free.
> All the best,
> Ray
> Ray Luo, Ph.D.
> rayluo.rayluolab.org
>
> -------- Original Message --------
> Subject: [AMBER] error during the calculation of MMPBSA
> From: Jeyaram R A
> To: amber.ambermd.org
> CC:
>
> Dear Amber Users,
> I did the 50ns MD simulation of protein-ligand complex
> system by using ff14SB force field for protein and glycam force field for
> ligand (sialic acid). From the output trjectories I am trying to
> calculate the MM-PBSA binding free erergy of this complex system. During
> the calculation i have the error as "CalcError:
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with prmtop
> comp.top!
> PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh" .
> In that following I am attaching the ligand pdb file and the output of the
> terminal. Help me to solve this error.
> MMPBSA.py -O -i mmpbsa.in -o 1.out -sp 1.prmtop -cp comp.top -rp prot.top
> -lp lig.top -y md1_50.nc
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> cpptraj found! Using /home/vit/Documents/amber16/bin/cpptraj
> Preparing trajectories for simulation...
> 1500 frames were processed by cpptraj for use in calculation.
> Running calculations on normal system...
> Beginning PB calculations with
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/home/vit/Documents/amber16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.
> py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calcu
> lation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calcu
> lation.py", line 433, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with
> prmtop comp.top!
> PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh
> Exiting. All files have been retained.
>
> Thanks in advance
> with regards
> R. A. Jeyaram
> Research scholar
> Vellore Institute of Technology
> Tamil Nadu, India.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Thomas Gaillard
Professeur assistant
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
France
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://thomasgaillard.fr
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 07 2019 - 03:00:02 PDT
