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Amber 10 Tutorial. antechamber: strange molecules get parameter files. antechamber & leap. antechamber 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. sustiva.pdb.

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Amber 10 tutorial

Amber 10 Tutorial

antechamber: strange molecules get parameter files


Antechamber leap
antechamber & leap

  • antechamber 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.


Sustiva pdb
sustiva.pdb

  • ATOM 1 C1 SUS 1 0.728 1.403 0.255

  • ATOM 2 H1 SUS 1 -0.136 1.756 0.782

  • ATOM 3 C2 SUS 1 0.803 0.080 -0.150

  • ATOM 4 C3 SUS 1 -0.290 -0.932 0.158

  • ATOM 5 C4 SUS 1 -1.635 -0.352 0.032

  • ATOM 6 C5 SUS 1 -2.718 0.123 -0.062

  • ATOM 7 C6 SUS 1 -4.044 0.695 -0.177

  • ATOM 8 H2 SUS 1 -4.741 0.335 0.558

  • ATOM 9 C7 SUS 1 -4.600 1.013 -1.541

  • ATOM 10 H3 SUS 1 -5.646 0.820 -1.697

  • ATOM 11 H4 SUS 1 -3.975 0.806 -2.390

  • ATOM 12 C8 SUS 1 -4.207 2.123 -0.629

  • ATOM 13 H5 SUS 1 -4.981 2.699 -0.155

  • ATOM 14 H6 SUS 1 -3.314 2.676 -0.858

  • ATOM 15 C9 SUS 1 -0.117 -1.500 1.582

  • ATOM 16 F1 SUS 1 1.056 -2.097 1.693

  • ATOM 17 F2 SUS 1 -0.170 -0.536 2.480

  • ATOM 18 F3 SUS 1 -1.047 -2.380 1.866

  • ATOM 19 O1 SUS 1 -0.232 -2.048 -0.712

  • ATOM 20 C10 SUS 1 0.893 -2.538 -1.245

  • ATOM 21 O2 SUS 1 0.922 -3.624 -1.713

  • ATOM 22 N1 SUS 1 1.964 -1.696 -1.242

  • ATOM 23 H7 SUS 1 2.776 -2.054 -1.692

  • ATOM 24 C11 SUS 1 1.919 -0.369 -0.836

  • ATOM 25 C12 SUS 1 2.963 0.503 -1.114

  • ATOM 26 H8 SUS 1 3.826 0.154 -1.653

  • ATOM 27 C13 SUS 1 2.892 1.817 -0.700

  • ATOM 28 H9 SUS 1 3.697 2.494 -0.911

  • ATOM 29 C14 SUS 1 1.772 2.262 -0.018

  • ATOM 30 Cl1 SUS 1 1.678 3.924 0.495

What 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.


Antechamber
antechamber

  • to generate the amber PREP files for sustiva (later used by leap to generate the parameter files) we run antechamber.

    • >> antechamber -i sustiva.pdb -fipdb -o sustiva.prepin -foprepi -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 system

        • bcc: BCC (AM1-BCC) used to calculate charges of the atoms

      • -s: this sets the verbosity of the output from antechamber

  • These output options can be seen in the “Amber10Tools.pdb” on pg 66 & 67.


Antechamber outputs
antechamber outputs

  • Note: 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* 8 ATOMTYPE.INF 4 sus.leap

    4 ANTECHAMBER_AC.AC 4 delete.com* 92 sustiva.crd

    4 ANTECHAMBER_AC.AC0 4 divcon.pdb 4 sustiva.frcmod

    4 ANTECHAMBER_AM1BCC.AC 16 leap.log 4 sustiva.pdb

    4 ANTECHAMBER_AM1BCC_PRE.AC 4 mopac.in 4 sustiva.prepin

    4 ANTECHAMBER_BOND_TYPE.AC 40 mopac.out 376 sustiva.top

    4 ANTECHAMBER_BOND_TYPE.AC0 4 mopac.pdb 164 sustivawh2o.lpdb

    4 ANTECHAMBER_PREP.AC 4 NEWPDB.PDB

    4 ANTECHAMBER_PREP.AC0 4 PREP.INF


Parmchk
parmchk

  • parmchk is used to check the parameters in our newly generated sustiva.prepin file.

    • >> parmchk -isustiva.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.


Now to leap
Now to LEAP

  • I 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 gaff

    • source leaprc.ff03

    • source leaprc.gaff

      • gaff is a force-field set used for antechamber and can be used in conjunction with other force-fields.


In leap
in LEAP

  • Then we load our sustiva information into leap from out sustiva.prepin file generated earlier:

    • loadamberprepsustiva.prepinpg 45 tools

      • loadamberprep 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)


In leap1
in LEAP

  • now check if everything is o.k. with our SUS unit.

    • check SUS

      • Checking 'SUS'....

      • Checking parameters for unit 'SUS'.

      • Checking for bond parameters.

      • Checking for angle parameters.

      • Could not find angle parameter: ca - c3 - c1

      • Could not find angle parameter: c1 - c1 - cx

      • Could not find angle parameter: c1 - cx - hc

      • Could not find angle parameter: c1 - cx - cx

      • Could not find angle parameter: c1 - cx - cx

      • There 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.


In leap2
in LEAP

  • To fix your angle parameter problem we load in our modified force field file that parmchk has given us (sustiva.frcmod).

    • loadamberparamssustiva.frcmod pg 45 tools

      • this 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 unit

    • check SUS

    • Checking 'SUS'....

    • Checking parameters for unit 'SUS'.

    • Checking for bond parameters.

    • Checking for angle parameters.

    • Unit is OK.

  • Now our SUS unit is O.K!


Output parameter files and pdb
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.crd

    • savdpdb SUS sustiva.lpdb

  • Finished! You can now run MD on this weird molecule.


Tutorial directory and links
tutorial directory and links

  • All the files for this tutorial can be found on [email protected]:~/Quickgo/amber10tutorial/antechamber/

  • The 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: http://hpce.iitm.ac.in/Manuals/Amber9_Tutorial/antechamber/index.htm


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