Respected Prof. Ray Luo
Thank you for your suggestion. I have two questions
1. I am using the same keywords in PB calculation of gaff force field, it is working well. But the error ocured in the case of glycam force field. Anyway i am adding the keyword radiopt=o.
2. How to update the latest version of amber
Thanks in advance
________________________________
From: rluo.uci.edu <rluo.uci.edu>
Sent: Tuesday, August 6, 2019 7:20:54 PM
To: AMBER Mailing List
Subject: Re: [AMBER] error during the calculation of MMPBSA
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.
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Received on Tue Aug 06 2019 - 08:30:02 PDT
