From owner-nwchem-users Tue Jul 25 14:53:05 2000 Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.8.8+Sun/8.8.5) id OAA16875 for nwchem-users-outgoing; Tue, 25 Jul 2000 14:44:07 -0700 (PDT) Date: Tue, 25 Jul 2000 14:42:54 -0700 From: "Vorpagel, Erich R" Subject: RE: Does anyone know how to add counter ions in NWCHEM 3.3.1? To: "'Matthew Lee'" , NWChem help Message-id: MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-type: text/plain; charset="iso-8859-1" Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Greetings Mathew, The 3.3.1 version of NWChem requires you go through a two step process to as counter ions. Here is an excerpt from an example for a protein with a single negative charge, thus, it needs one sodium ion to balance to neutrality. You will need to modify the NWChem input files according to your own molecule. Basically, the .seq file must be generated, then edited to include the counter ions. Then a new topology and restart file must be created. The next release (version 4.0) will add counter ions by default and does not require editing the .seq file. Topology and Restart file preparation: Generate initial files: 1. Use a text editor to create the following simple NWChem input file for running the "Prepare" task on the protein, call it my2ifbI.nw: Title; Preparation of Fatty Acid Binding Protein start holo prepare system ent2ifb_em source pdb amber end; task prepare prepare read rst ent2ifb_em.rst write pdb ent2ifbI.pdb end; task prepare 2. Run the above file using the command: nwchem my2ifbI.nw > my2ifbI.nwout 3. The output will be written to a file. This time the task should complete without error. Add Counter ions and relax hydrogen atoms: 1. To determine the total charge for the protein/ligand complex, you need to look at the NWChem output file. You can either use a text editor to look for the line containing "Total charge" or you can use the Unix grep command: grep "Total charge" my2ifbI.nwout 2. You should end up with a net negative one charge. So you need to add one sodium ion. 3. Before going on to the next step, the sequence file, ent2ifb.seq created in the previous section must be edited to include the sodium ion. Use a text editor to modify the end of the file to look like this: molecule 133PLM molecule # These lines must 134Na # be added. solvent 0spce stop 4. Use a text editor to create the following NWChem input file to prepare a new topology file and PDB file containing the sodium ion. Call it my2ifbNa.nw: Title; Fatty Acid Binding Protein -- Add counter ion. memory heap 1 mb stack 64 mb global 24 mb start holo prepare system ent2ifb_em grid 24 0.5 # Generates grid to determine best place for counter ion. new_top end; task prepare md system ent2ifb_em fix non-H # Fix all heavy atoms sd 100 init 0.01 min 1.0E-4 max 0.1 cg 1000 init 0.01 min 1.0E-8 cy 10 noshake # make sure the hydrogen atoms can move. end; task md optimize prepare read rst ent2ifb_em.qrs # Save the resulting minimized structure. write pdb ent2ifbNa.pdb end; task prepare 5. Run the above file using the command: nwchem my2ifbNa.nw > my2ifbNa.nwout 6. After about 12-15 minutes, the job should complete. Look at the output file to determine whether there were any errors. Add solvent and relax the system: 1. Before going on to the next step, the ent2ifbNa.pdb file must be renamed to ent2ifb.pdb so the counter ion is included. Use the command: mv ent2ifbNa.pdb ent2ifb.pdb 2. Use a text editor to create the following NWChem input file to prepare a set of files which will include solvent molecules. Call it my2ifbSolv.nw: Title; Fatty Acid Binding Protein -- Add counter ion. memory heap 1 mb stack 64 mb global 24 mb start holo prepare system ent2ifb_em solvate # adds water molecules touch 0.13 # minimum distance for solvent expand 0.10 # expand cube after solvating center; orient new_top new_seq end; task prepare # Copy restart file for the following task. task shell "cp ent2ifb_em.rst ent2ifb_md1.rst" md system ent2ifb_md1 cutoff 0.9 vreass 10001 300.0 # assign random velocities, once. leapfrog equil 0 data 500 time 0.0 step 0.0020 isotherm 300.0 trelax 0.1 isobar 101250.0 trelax 0.4 compres 4.53E-10 shake 100 100 0.0010 0.0010 fix solute # Relax solvent while solute fixed. print step 100 extra stat 1000 update pairs 10 center 0 motion 0 record rest 100 record coord 0 scoor 0 veloc 0 svelo 0 record prop 0 sync 0 load pairs end; task md dynamics # Copy restart file for the following task. task shell "cp ent2ifb_md1.rst ent2ifb_em1.rst" md system ent2ifb_em1 unfix all fix solvent # Hold solvent molecules fixed and relax solute. sd 500 init 0.01 min 1.0D-4 max 0.1 noshake end; task md optimize prepare read rst ent2ifb_em1.qrs # Save the relaxed structure as a PDB file write pdb ent2ifbSolv.pdb write rst ent2ifbSolv_em.rst end; task prepare 3. Run the above file using the command: nwchem my2ifbSolv.nw > my2ifbSolv.nwout 4. After about 40 minutes, the job should complete. Look at the output file to determine whether there were any errors. -----Original Message----- From: Matthew Lee [SMTP:mlee@adrik.bchs.uh.edu] Sent: Tuesday, July 25, 2000 10:12 am To: NWChem help Subject: Does anyone know how to add counter ions in NWCHEM 3.3.1? Hello, I have been pouring through the NWChem 3.3.1 manual, but all I could find about counter ion was a tinny little phrase in a paragraph that describes the solvation function of the prepare module. It only says that prepare will add the counter ions to the topology and restart but no explicit instructions on how to do that. If anyone knows the answer to that, could you please help me out? Thanks =========================================== --@_@-- Matthew Lee V Graduate Research Assistant Department of Biochemical & Biophysical Sciences University of Houston (713) 743-8367 e-mail: mlee@adrik.bchs.uh.edu http://adrik.bchs.uh.edu/~mlee ===========================================