Presentation on theme: "antechamber: strange molecules get parameter files"— Presentation transcript:
1 antechamber: strange molecules get parameter files Amber 10 Tutorialantechamber: strange molecules get parameter files
2 antechamber & leapantechamber is predominantly a file converter. However, it can be used in conjunction with leap to build parameter files that can be used to run MD and other simulations.
3 sustiva.pdbATOM C1 SUSATOM H1 SUSATOM C2 SUSATOM C3 SUSATOM C4 SUSATOM C5 SUSATOM C6 SUSATOM H2 SUSATOM C7 SUSATOM H3 SUSATOM H4 SUSATOM C8 SUSATOM H5 SUSATOM H6 SUSATOM C9 SUSATOM F1 SUSATOM F2 SUSATOM F3 SUSATOM O1 SUSATOM C10 SUSATOM O2 SUSATOM N1 SUSATOM H7 SUSATOM C11 SUSATOM C12 SUSATOM H8 SUSATOM C13 SUSATOM H9 SUSATOM C14 SUSATOM Cl1 SUSWhat makes the antechamber/leap combination so powerful is the original format of the information that is fed into it.Notice that on the left there is no detailed information given. Only atom #, atom type, and position. With this antechamber and leap can generate parameter files.The SUS label on the atoms here is important because it will be the label leap will use later for the sustiva unit.
4 antechamberto generate the amber PREP files for sustiva (later used by leap to generate the parameter files) we run antechamber.>> antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2-i: means input file-fi: means input file format (which is pdb in this case)-o: the name we wish the output file to have-fo: the format we wish the output file to have-c: the charge method we wish to use to build charges for out SUS systembcc: BCC (AM1-BCC) used to calculate charges of the atoms-s: this sets the verbosity of the output from antechamberThese output options can be seen in the “Amber10Tools.pdb” on pg 66 & 67.
5 antechamber outputsNote: antechamber will create a lot intermediate files. These files will all be CAPITALIZED and can be deleted. They are only useful if something went wrong in antechamber.Also some divcon files will be generated. They are used to show how the charges of the atoms were found via quantum mechanics.4 AchamberSUS.sh* ATOMTYPE.INF 4 sus.leap4 ANTECHAMBER_AC.AC delete.com* sustiva.crd4 ANTECHAMBER_AC.AC divcon.pdb sustiva.frcmod4 ANTECHAMBER_AM1BCC.AC leap.log sustiva.pdb4 ANTECHAMBER_AM1BCC_PRE.AC 4 mopac.in sustiva.prepin4 ANTECHAMBER_BOND_TYPE.AC mopac.out sustiva.top4 ANTECHAMBER_BOND_TYPE.AC mopac.pdb sustivawh2o.lpdb4 ANTECHAMBER_PREP.AC NEWPDB.PDB4 ANTECHAMBER_PREP.AC PREP.INF
6 parmchkparmchk is used to check the parameters in our newly generated sustiva.prepin file.>> parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod-i: means input file-f: means input file format (which is prepi in this case)-o: the name we wish the output file to have*.frcmod is a force-field modification file. This will contain missing or all forcefields that are needed for you system.These output options can be seen in the “Amber10Tools.pdb” on pg 68.
7 Now to LEAPI will assume you have read the leap tutorial or have basic understanding of leap here.Normally we load one set of force-field parameters into leap. However with antechamber we load our generic ff03 and also gaffsource leaprc.ff03source leaprc.gaffgaff is a force-field set used for antechamber and can be used in conjunction with other force-fields.
8 in LEAPThen we load our sustiva information into leap from out sustiva.prepin file generated earlier:loadamberprep sustiva.prepin pg 45 toolsloadamberprep loads in an amber prepin file. The key here is that a new unit is created for every “residue” in the prepin file. i.e. You would have more units if you had more than 1 type of label for objects in your original pdb file.If you type “list” in leap now you will see a unit titled SUS listed. This unit is labeled SUS because it was labeled this in the original pdb file (sustiva.pdb)
9 in LEAP now check if everything is o.k. with our SUS unit. check SUSChecking 'SUS'....Checking parameters for unit 'SUS'.Checking for bond parameters.Checking for angle parameters.Could not find angle parameter: ca - c3 - c1Could not find angle parameter: c1 - c1 - cxCould not find angle parameter: c1 - cx - hcCould not find angle parameter: c1 - cx - cxThere are missing parameters.Unit is OK.I believe the program is lying to you here, unit is NOT o.k. :P.Could not find angle parameter: … is a bad thing.
10 in LEAPTo fix your angle parameter problem we load in our modified force field file that parmchk has given us (sustiva.frcmod).loadamberparams sustiva.frcmod pg 45 toolsthis will load the parameters contained within the file sustiva.frcmod into the general amber parameters. these will be used if needed by any unit.Now recheck the SUS unitcheck SUSChecking 'SUS'....Checking parameters for unit 'SUS'.Checking for bond parameters.Checking for angle parameters.Unit is OK.Now our SUS unit is O.K!
11 Output parameter files and pdb Now we just output our new parameter file and save a copy of our pdb.saveamberparm SUS sustiva.top sustiva.crdsavdpdb SUS sustiva.lpdbFinished! You can now run MD on this weird molecule.
12 tutorial directory and links All the files for this tutorial can be found onThe shell script AchamberSUS.sh will use the one file sustiva.pdb to do all of the above steps quickly and should be referenced to quickly see the commands needed.delete.com will delete all of the files generate by this process and will allow you to start over again for practice.A very well written tutorial on this process can also be found on the net at: