Hello friends.
As a part of one work, I have done molecular docking to explain the in vitro results. I have confirmed the ligand - protein interaction through ITC, Spectrophotometer and enzyme kinetics. Since I used rigid docking method to explain the binding mode, I performed MD simulation (50 ns) too see the residence of time of the ligand in the binding site of protein. I have used MM-GBSA method to calculate the binding free energy. I have performed the MD simulation using Desmond and communicated the whole results to a journal. The only comment from the reviewer was to perform MM-PBSA calculation using the MD trajectory and to calculate the ligand decomposition analysis. Some one please guide me how to do it. Also I have one specific question
1. Is it possible to calculate the MM-PBSA from the Desmond trajectory using VMD?
Some please guide me. Thank you
I don't think you can do MM-PBSA calculations in VMD. However, there are other software that can do these calculations, for example, see the following link:
http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
Dear Kamberaj
Thanks for the answer. It's possible to do with g_mmpbsa. But the problem is to convert the Desmond trajectory file to gromacs format.
Hi Dileep,
You should check the following links:
https://github.com/shirtsgroup/InterMol
https://groups.google.com/forum/#!msg/desmond-md-users/vy1VvhBMyi8/oE74BTtdAwAJ
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html
Hello Ishikawa san
Thanks for suggesting those links. Unfortunately, none of these are working for Desmond to convert to any format. I have already done those things before. Since it was not working I posted it. I don't how to proceed further. it is almost impossible to re run the whole simulations in gromacs or amber sincere there are a lot of systems. It is possible to convert the trajectory file using VMD. But I cannot make the topology file. I think it is also possible to make the MD simulations parameters..but only problem is the topology file.
Hi Dileep.
Can you make a topology file for GROMACS from an original PDB file?
I also recommend MMPBSA.py module in AmberTools.
Hello Ishikawa san
If I am making the topology file with original pdb, it may be different from the protein in the trajectory because the force field used for Desmond run was opls 2005 and there is no such force field in gromacs. So the charges and atom types will be different in both file formats. Even if I am using Mm-pbsa.py, it cannot handle the Desmond files.
Hi again,
You should do MD simulations again by pmemd.cuda module of AMBER installed in HPC at your institute.
Yes I am planning to redo it again with gromacs or AMBER. Thanks for the supports and suggestions
Hi Dileep, could you figure out a way to do mm-pbsa calculations on desmond trajecories?
thermal_mmgbsa.py script can do mm-gbsa calculations.
Hi Rajiv
There are some scripts available in the Schrodinger site to calculate MM-GBSA from the trajectory files. If you are not able to find it from the site I will send you on Monday
hi Dileep
Can you please send me some scripts in the Schrodinger site to calculate MM-GBSA from the trajectory files ?
Hello Dileep Vijayan ,
Can you please send me the scripts of Schrodinger to calculate MM-GBSA from the trajectory files? Do this script need a different license or a regular license file can be OK? I am trying to do it but it is showing "Fatal 1: Could not find a license file." My email address is [email protected]. Please send me the script and how to do it.
Hello All,
Hope this would help answer some of the queries raised before.
For the details of the scripts to run Molecular Dynamics related jobs in Schrodinger go through the links attached below.
https://www.schrodinger.com/scriptcenter?f%5B0%5D=field_command_line_script_type%3A1119
Of course you can do this.
thermal_mmgbsa.py is in $SCHRODINGER/mmshare-vxxxxx/python/common
run it as below:
$SCHRODINGER/run thermal_mmgbsa.py
Dear all.,
Is there any version of SCHRODINGER can run with CPU not GPU?
Thanks in advance
Sepideh Parvizpour according what I know, Schrodinger versions of 2018-4 and earlier can run over CPU.
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