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-- Gustavo Seabra. On Tue, Nov 8, 2022 at 9:38 AM Clorice Reinhardt <clorice.reinhardt.yale.edu> wrote: > Hi Gustavo, > > Are you using a bonded model for the water oxygen? You should try using a > non-bonded model, as i've run into this before, and using nonbonded > approach for the waters worked wonderfully and Pengfei detailed the > solution and cause to this problem in the tutorial (see bottom of the page) > > http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm > > All the best, > Clorice > > On Fri, Nov 4, 2022 at 10:07 PM Gustavo Seabra via AMBER < > amber.ambermd.org> wrote: > >> Hi everyone, >> >> I'd really appreciate some help figuring out what I'm doing wrong here. >> >> TLDR: I created a system using MCPB.py, and as soon as MD simulation >> starts, one water molecule collapses with another residue in the metal >> center, and the simulation blows up. I appreciate any help I can get to >> solve this problem. Thanks! >> >> Details: >> I have a metalloprotein in which the Fe(II) center coordinates to 2 HID, 1 >> ASP and 1 water, and I used MCPB.y to create the parameters for MD. The >> procedure I followed was: >> >> Starting from an apo-protein prepared in Maestro, the treated with >> pdb4amber, >> $ grep FE apo-protein_pdb4amber.pdb > FE.pdb >> $ grep WAT apo-protein_pdb4amber.pdb > WAT.pdb >> $ metalpdb2mol2.py -i FE.pdb -o FE.mol2 -c 2 >> >> # Create parameters for the water: >> $ antechamber -i WAT.pdb -fi pdb -o gaussian_WAT.com -fo gcrt -gv 1 -ge >> WAT.gesp -eq 2 -rn WAT -pf Y >> (Run g09. Note: I use Gaussian09 because the files from Antechamber were >> prepared for it.) >> $ antechamber -i WAT.gesp -fi gesp -o WAT_resp.mol2 -fo mol2 -c resp -eq 2 >> -rn WAT -at amber -pf y >> $ ln -s WAT_resp.mol2 ./WAT.mol2 >> $ cp $AMBERHOME/dat/leap/parm/frcmod.opc . >> >> # Now, run MCPB.py >> $ MCPB.py -i MCPB.in -s 1 2>&1 | tee mcpb_s1.log >> (Run g16 calculations for the complexes as created by MCPB.py >> Note: I here use Gaussian16, and just alter the SCF algorithm to SCF=YQC, >> which is a newer method suitable for large systems.) >> $ MCPB.py -i MCPB.in -s 2 2>&1 | tee mcpb_s2.log >> $ MCPB.py -i MCPB.in -s 3 2>&1 | tee mcpb_s3.log >> $ MCPB.py -i MCPB.in -s 4 2>&1 | tee mcpb_s4.log >> >> # Modify protein-FE_tleap.in file to >> 1. Use solvateOct with 15A buffer, >> 2. Add `check mol` to get the charges >> 3. Stop after adding waters, so we can calculate the >> number of ions to add. >> 4. Add 'verbosity 2' after sourcing force fields >> 5. Change save commands to save NetCDF files and extensions >> `.ncrst` and `.parm7` >> >> The charge was +7.0, and 24,718 waters were added. So, >> add the following line to protein-FE_tleap.in: >> `addIonsRand mol NA 63 CL 70` >> Now, run it fully to create the system. >> >> # Finally, create the parameters with LEaP >> $ tleap -s -f protein-FE_tleap.in 2>&1 | tee protein-FE_tleap.log >> >> LEaP creates the files with some warnings, but no errors. With those last >> files, I starting an MD protocol where I first run a sequence of >> minimizations where I start with the protein and metal center (including >> the coordinated water) restrained with a constant of 100 kcal/(mol.A)^2, >> then I remove the restraints gradually in a series of minimizations, to >> finally run a small 100 K MD and then start heating the system. >> >> The problem is that as soon as the restraints are weak enough, the system >> collapses. One hydrogen of the coordinated water just sinks into one ASP >> oxygen, and the simulation blows up. >> >> I suppose I must be doing something wrong here, but I really can't figure >> out what is wrong. Does anyone here see what I'm missing? I really >> appreciate any help. I attached here the input I'm using for MCPB.py. I'll >> be happy to provide more information if anyone needs it. >> >> Thanks a lot! >> -- >> Gustavo Seabra. >> _______________________________________________ >> 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/amberReceived on Tue Nov 08 2022 - 12:30:02 PST