Re: [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 22 Sep 2015 11:28:45 -0700

The warning informations are just for your reference as you pointed
out. So you can successfully complete the runs?

All the best,
Ray
--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Sep 21, 2015 at 7:15 PM, 杨川 <junaid.hust.edu.cn> wrote:
> Thank you so much for the instant help.. I put the suggested value in my input file ( inp=1, radiopt=0 ).  Now it end with some warning message. but these warning message are just informational messgaes.
>
> Now My input file is..
>
> Input file for running PB and GB in serial
> &general
>    endframe=50, keep_files=2,
> strip_mask=":WAT,CL-,Na+",
> /
> &gb
>   igb=2, saltcon=0.100,
> /
> &pb
>   istrng=0.100, inp=1, radiopt=0
> /
>
>
> -----Original Messages-----
> From: "杨川" <junaid.hust.edu.cn>
> Sent Time: Monday, September 21, 2015
> To: amber.ambermd.org
> Cc:
> Subject: Problem In Performing MMPBSA Calculation for System containing Ligand and Protein
>
> Dear Amber Users
>
> I have simulated the complex using amber14 with GPU. I have got problem while running the MMPBSA.py . I have got this problem with several complexes.
>
> I used this commond
> MMPBSA.py -O -i mmpbsa_2b.in -o final.dat -sp com_solvated.top -cp com.top -rp rec.top -lp lig.top -y *.mdcrd
>
> My input file is..
>
> Input file for running PB and GB in serial
> &general
>    endframe=50, keep_files=2,
> strip_mask=":WAT:CL-"Na+",
> /
> &gb
>   igb=2, saltcon=0.100,
> /
> &pb
>   istrng=0.100,
> /
>
> the error message said.....
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /opt/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /opt/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /opt/amber14/bin/mmpbsa_py_energy
>   calculating complex contribution...
>   calculating receptor contribution...
>   calculating ligand contribution...
>
> Beginning PB calculations with /opt/amber14/bin/mmpbsa_py_energy
>   calculating complex contribution...
>   File "/opt/amber14/bin/MMPBSA.py", line 104, in <module>
>     app.run_mmpbsa()
>   File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 416, in run
>     self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /opt/amber14/bin/mmpbsa_py_energy failed with prmtop com.top!
>     PB Bomb in pb_aaradi(): No radius assigned for atom    11  CB    2C
>
> Exiting. All files have been retained
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Received on Tue Sep 22 2015 - 11:30:03 PDT
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