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6 Jan 2021: 2. Sample section of the input for a charmm run:. OPEN UNIT 20 FORM NAME protein_new.pdb READ! ... Excuse the lack of docu for this program ;-) Then paste the new coordinates into your newly-made.

The bottom of output should look like this:. getallpaths> writing data for new ts to ts.data getallpaths> writing data for 1 new minima to min.data getallpaths> writing data for ... writing data for 1 new minima to min.data setup> The unique A and B

Files min.[A,B,data].fastest, ts.data.fastest,points.[min,ts].fastest: a new database containing only the stationary points on the fastest path. ... connect them, and all the individual stationary points in those groups will be written to new.

6 Jan 2021: export AMBERHOME=/home/$USER/svn/AMBERTOOLS. Exit vi and then source the file you just altered to export the new variable:. ... Old $PATH:. export PATH=$PATH:/home/csw34/scripts. New $PATH. export PATH=$PATH:/home/csw34/scripts:$AMBERHOME/exe. Once you

6 Jan 2021: 5.5-dev. Branched from trunk on the 25-Mar-10. New program: res2disp added. ... Kernel integrals constructed in CamCASP. New propagator module: Implements the ALDA(X) kernel in the manner described in Bukowski et al.

CHARMM> CLOSE UNIT 20 VCLOSE: Closing unit 20 with status "KEEP" $$$$$$ New timer profile $$$$$ Total time 0.34631 Other: 0.00000 NORMAL TERMINATION BY END OF FILE MAXIMUM STACK

PATHSAMPLE then attempts to connect A and B and will repeat this until it finds a new minimum that reconnects A and B (this is however very unlikely to happen).

6 Jan 2021: New backup system. I want to buy a new backup server with about 6Tb of space, move the backups onto that, and make them user-accessible. ... New archive system. The other two old backup servers would immediately be free for reuse.

6 Jan 2021: to save the ligand you are editing as a new PDB using File>Save and changing the type to. ... R<CILE 385> Created a new atom named: O2 within residue:. R<CILE 385> Added missing heavy atom:.

Unfortunately, the new version of the converter does not accept this and so you need to use the correct hex code instead in pstoimg.pin, #D9D9D9.

to save the ligand you are editing as a new PDB using File>Save and changing the type to. ... R<CILE 385> Created a new atom named: O2 within residue:. R<CILE 385> Added missing heavy atom:.

cp perm.allow COPTIM. Finally, we need to create a new file, odata, the OPTIM input file. ... You will notice that a lot of new files have been created in the directory.

Run the following code and the new file coords.prmtop.ni is a topology file that includes all internal rigid body interactions:. ... For every new rigid body this list needs to be updated.

6 Jan 2021: This information is used to set up UCS computer accounts in advance and is needed for any new member of staff.

It has a strong focus on an object oriented & modular design which makes it very powerful to try new functionality.

6 Jan 2021: For the new topology file, the energy is invariant to permutation of the aforementioned atoms or groups :). ... How do I use it? /perm-prmtop.py name-of-topology-file name-of-new-topology-file. Where can I find it?

Computer Office services. From Docswiki. This has moved to the COs' wiki. COs only! And even more recently, this has gone public on (Raven password needed, but if you got here then you already have one). Retrieved from "". Navigation menu. Personal

You should now have three new files in your directory - rbodyconfig and coordsinirigid are described above. ... First, lets copy the OPTIM points.final.pdb file for the complex into two new files which we can edit:.

For the new topology file, the energy is invariant to permutation of the aforementioned atoms or groups :). ... How do I use it? /perm-prmtop.py name-of-topology-file name-of-new-topology-file. Where can I find it?

6 Jan 2021: General queueing problems. From CUC3. This page is for general queueing discussion. There are specific pages for discussing mek-quake and tardis. I have moved the paragraph from the page for me-quake as it is more appropriate here. --Catherine 09:55,

In that sense, mercurial is very similar to the other new generation version management systems as git or bazaar. ... Also good. Since all new code that you write has bugs, you have a choice.

6 Jan 2021: perl -pi -e 's/old string/new string/' list_of_files. is equivalent to. for file in list_of_files; do sed -e 's/old string/new string/' $file > tmp mv

6. next step: creation new binary file points.ts; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

6 Jan 2021: Adding a model to GMIN. From CUC3. This is rough outline of the subrounties that need to be changed to add a new model to GMIN.

Zippo Sicortex machine. From Docswiki. Please record useful notes about the new SiCortex machine here.

6 Jan 2021: 6. next step: creation new binary file points.ts; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

6 Jan 2021: a symbolic link to the file's new location and leaving all other files untouched.

It is not meant to be a replacement for them, but rather as a playground for quickly testing new ideas, finding optimal parameters for the various routines in GMIN and OPTIM, ... You can also generate interactive disconnectivity graphs, which can be used

6 Jan 2021: Adding a model for PATHSAMPLE. From CUC3. Under Construction. This is rough outline of the subrounties that need to be changed to add a new model to GMIN. ... connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466 00:24, 8 July

These have to be renamed in DMACRYS! UPDATE: the new PGI is slightly better, but as Davids recommends, don't use PGI! ... Moves via XML. This idea has been cancelled, use new Python interface instead I'm thinking of implementing a move protocol using an

6 Jan 2021: I should find a concrete example that compares the old and new, but till I do that, here are some numbers for a calculation done on the new quad-core machine

Adding a model to GMIN. From Docswiki. This is rough outline of the subrounties that need to be changed to add a new model to GMIN.

6 Jan 2021: Eventually additions of new connections to the database will no longer reduce the rate constant.

It should be omitted from new code. IARGC. subroutine iargc_subr(n) integer, intent(out) :: n.

6 Jan 2021: KNOPPIX_remastered | nice -5. /create_compressed_fs - 65536 > masterISO/KNOPPIX/KNOPPIX. Then boot up SuSE and copy the new compressed file over your old /KNOPPIX/KNOPPIX. ... Boot the knoppix system to test the new KNOPPIX file. Keep going round and

Adding a model for PATHSAMPLE. From Docswiki. Under Construction. This is rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE. ... connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466

6 Jan 2021: 100% (3/3) done refs/remotes/origin/master: fast forward to branch 'master' of file:///Users/athom/tmp/git/tmp/Cambridge old.new: 880aefd.62b3628 Merge made by recursive.

KNOPPIX_remastered | nice -5. /create_compressed_fs - 65536 > masterISO/KNOPPIX/KNOPPIX. Then boot up SuSE and copy the new compressed file over your old /KNOPPIX/KNOPPIX. ... Boot the knoppix system to test the new KNOPPIX file. Keep going round and

6 Jan 2021: Running out of space on existing JBODs. Workstations tend to contain archives of old user accounts because new users need old users' data (or PI wants to hang onto it) but ... So we need a gigantic new JBOD to accomodate the growing data.

Running out of space on existing JBODs. Workstations tend to contain archives of old user accounts because new users need old users' data (or PI wants to hang onto it) but ... So we need a gigantic new JBOD to accomodate the growing data.

6 Jan 2021: This causes many "interesting" issues when I attempted to use the RESTART files for new calculations.

I should find a concrete example that compares the old and new, but till I do that, here are some numbers for a calculation done on the new quad-core machine

6 Jan 2021: I need a new version of the image without those SuSE libs to use on these machines. ... The auto-patching script doesn't do kernels on 10.2 so it will always need a computer officer's intervention to do a new kernel anyway.

Add stuff you'd like in the new image here. gaim (chat client). ... OpenOffice.org (Office suite). OpenSSH (SSH client). Pan (news client). Pine (mail/news client).

6 Jan 2021: filestatus = character(3): OLD/old or NEW/new or OVR/ovr or ADD/add! NEW: This is a new file to be opened! ... NEW). In the latter case, any existing file by the same name is over-written!

ajwt3/code/qchem/qcsetup.bash. H. 2. O test. create a new directory with the following files h2o.inp.

6 Jan 2021: These variables will now be automatically set when you open a new shell, but for now, we need to load them manually. ... Whenever you introduce a new keyword or feature, it should be documented.

Please feel free to contribute new tests and to improve the old ones! ... If you are absolutely certain that your changes have made the code better, you should replace the expected_output folder with your new output files and commit the changes.

6 Jan 2021: Talks should last around 40 minutes to allow for discussion. Some of us are quite new or unfamiliar with certain areas, so perhaps a bit of background will help. ... Stephen Jenkins (surface science group). For any remarks, suggestions or new additions

Copy the coords.prmtop and coords.inpcrd files you just made into a new directory, and add the following file:. ... For vacuum, use igb=0 and delete "saltcon" keyword. min_md.in - the AMBER (SANDER) settings for molecular dynamics (used to generate new