I would like to simplify the file preparation for MD with unigbsa. What should I do?

[Tangbbmc]

It is well-known that preparing the files for molecular dynamic (MD) simulation of protein-ligand complex is a tedious process, which includes preparing ligand topology, solvation, adding ions, energy minimization, equilibration, and so on. Could I simplify the file preparation for 100-ns gromacs MD run of one protein-ligand complex with unigbsa?

[Aunity]

Yes, you can just use the command unigbsa-md to do that, here is an example:

unigbsa-md -p 1ceb_protein.pdb -l 1ceb_ligand.sdf -pf amber99sb -lf gaff -bt cubic -d 1.0 -conc 0.15 -o md-100ns -nsteps 50000000 -nframe  10000 -nt 16

[Tangbbmc]

Great! Thank you very much for your reply! I love your software very much! However, I have some questions. The command unigbsa-md did not mention water model. Which water model will be selected for md simulation? Except for amber99sb force field for protein and -gaff force field for ligand, can I select other force fields for protein and ligand? I have installed GPU version of Gromac2024 on Ubuntu system? I hope that unigbsa invokes Gromacs2024 to speed simulation. What should I do? Finally, I run the following command based on your provided example, however some error happened. Could you give me some suggestions to solve this question? I am looking forward to your reply as soon as possible! (gbsa) ***@***.***:~/Final_NADP$ unigbsa-md -p com_rep.pdb -l final_NAP.mol2 -pf amber99sb -lf gaff -bt cubic -d 1.0 -conc 0.15 -o md-50ns -nsteps 25000000 -nframe 500 -nt 30 10/18/2024 23:08:30 PM - INFO - Build ligand topology: final_NAP. 10/18/2024 23:08:32 PM - INFO - Building simulation for: final_NAP. gmx mdrun -v -deffnm nvt -nt 30 -ntmpi 1 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3 32 90.0 0.3281 0.2211 0.0973 1 16 67.6 0.0973 0.0973 0.0973 2 20 90.0 0.1290 0.1202 0.0973 Wrote pdb files with previous and current coordinates Step 169, time 0.338 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.045649, max 2.363351 (between atoms 3 and 32) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3 32 90.0 0.2211 0.3273 0.0973 1 16 75.6 0.0973 0.0973 0.0973 2 20 90.0 0.1202 0.1286 0.0973 Wrote pdb files with previous and current coordinates Step 170, time 0.34 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.026447, max 1.358207 (between atoms 3 and 32) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3 32 90.0 0.3273 0.2295 0.0973 1 16 63.6 0.0973 0.0973 0.0973 2 20 90.0 0.1286 0.1221 0.0973 Wrote pdb files with previous and current coordinates Step 171, time 0.342 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.157090, max 8.201681 (between atoms 3 and 32) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3 32 90.0 0.2295 0.8953 0.0973 1 16 71.7 0.0973 0.0973 0.0973 2 20 90.0 0.1221 0.1282 0.0973 Wrote pdb files with previous and current coordinates Step 172, time 0.344 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 32.763947, max 1711.896606 (between atoms 3 and 32) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3 32 122.9 0.8953 166.6649 0.0973 1 16 69.3 0.0973 0.0973 0.0973 2 20 90.0 0.1282 0.1232 0.0973 step 172: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) Traceback (most recent call last): File "/home/dell/anaconda3/envs/gbsa/bin/unigbsa-md", line 8, in <module> sys.exit(simulation_run()) ^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/CLI.py", line 231, in simulation_run mdgro, mdxtc, topfile = engine.run_to_md(grofile, topfile, rundir=None, boxtype=boxtype, boxsize=boxsize, conc=conc, nsteps=nsteps, nframe=nframe, nt=nt) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/mdrun.py", line 446, in run_to_md nptpdb, topfile = self.run_to_npt(pdbfile, topfile, rundir=rundir, boxtype=boxtype, boxsize=boxsize, maxsol=maxsol, conc=conc, nsteps=eqsteps, nt=nt) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/mdrun.py", line 425, in run_to_npt nvtpdb = self.gmx_nvt(minipdb, topfile, mdpfile=os.path.join(MDPFILESDIR, 'nvt.mdp'), nsteps=nsteps, nt=nt) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/mdrun.py", line 273, in gmx_nvt outfile = self._mdrun(outtpr, nt, nsteps=nsteps) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/mdrun.py", line 80, in _mdrun raise Exception('ERROR run mdrun %s. See the logfile for details %s'%(tprfile, os.path.abspath(self.gmxlog))) 唐王刚 Wanggang Tang 博士 副教授 Ph.D. Associate Professor Address: No. 2600, Donghai Avenue. Bengbu, Anhui, China Alternative email address: ***@***.*** Institution homepage: https://www.bbmc.edu.cn/ 发件人：Maohua Yang ***@***.***> 发送日期：2024-10-16 18:07:45 收件人：dptech-corp/Uni-GBSA ***@***.***> 抄送人：Wanggang ***@***.***>,Author ***@***.***> 主题：Re: [dptech-corp/Uni-GBSA] I would like to simplify the file preparation for MD with unigbsa. What should I do? (Issue #56) Yes, you can just use the command unigbsa-md to do that, here is an example: unigbsa-md -p 1ceb_protein.pdb -l 1ceb_ligand.sdf -pf amber99sb -lf gaff -bt cubic -d 1.0 -conc 0.15 -o md-100ns -nsteps 50000000 -nframe 10000 -nt 16 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>