You might try the one of these resources: 1) Check the PDB's ligand Expo: http://ligand-expo.rcsb.org/. If you can find an appropriate mmCif file, toppology and parameters can be generated using eginput/PSF_generation/genLigandCif.py. 2) ACPYPE http://bio2byte.be/acpype/ 3) The Dundee PRODRG2 Server http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg2. How do I make a cis-residue (such as cis-proile)?
After your PSF is read (via e.g. protocol.initStruct) or generated (via e.g. psfGen.seqToPSF or protocol.loadPDB), use psgGen.cisPeptide(startResid, segName) to make a cis peptide bond between residues startResid and startResid+1. Careful! By this definition startResid is one less than the residue you'd like to be a cis-residue. The segName argument can be omitted if there is a single segid in the structure. After calling cisPeptide, you can write out the updated PSF, which can be used in the future without another call to cisPeptide.3. script to add-in atoms whose positions are initially unknown
Here's a script which adds unknown atoms given some known positions. I'l send the resulting pdb file separately. Charles - -- Charles Schwieters email: Charles.Schwieters@nih.gov www: http://schwieters.org/cds phone: (301) 402-4914 FAX: (301) 402-2867 rtf @TOPPAR:topallhdg_new.pro end evaluate ($kbbang = 500.0) evaluate ($kbbimp = 500.0) ! ! building-on sidechains, given known bb atoms (from pdb file only). ! ! to use: change the line with input.pdb appropriately. ! Output will be in out.pdb ! ! set constraints to only calculate necessary interactions ! (don't calc bb-bb interactions) ! don't make the improper interactions too strong: will torque bonds, angles ! ! to try: turn off vwd entirely in stage1! ! ! script based on Nilges et.al. script for random starting coords ! ! CDS 7/8/02 ! param @TOPPAR:parallhdg_new.pro end segment name=" " SETUP=TRUE chain LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO } LINK PEPT HEAD - * TAIL + * END FIRSt PROP TAIL + PRO END { nter for PRO } FIRSt NTER TAIL + * END LAST CTER HEAD - * END SET ECHO=TRUE END coor @input.pdb end end delete select (name hd1 and resname his) end !remove all hydrogens! delete select (hydro) end write psf output=l.psf end param ! @TOPPAR:parallhdg_new.pro bond CP NH3 $kbon 1.473 ! CP - proline at N terminus angle CP CP NH3 $kang 103.2 ! CP - proline at N terminus angle HA CP NH3 $kang 109.5 ! CP - proline at N terminus angle CT NH3 CP $kang 112.0 ! CP - proline at N terminus improper HC HC CT CP 50.0 0 -70.0 ! N-term Pro improper HA HA CP NH3 $kchi 0 -70.874 ! CP methylene end coor @indira.pdb vector do (fbeta=10) (not known) {*Friction coefficient for MD heatbath.*} vector do (mass=100) (not known) {*Uniform heavy masses to speed*} vector do (fbeta=0) (known) {*Friction coefficient for MD heatbath.*} vector do (mass=0) (known) {*Uniform heavy masses to speed*} {*molecular dynamics. *} constraints fix (known) end vector do (vx = 0) (known) vector do (vy = 0) (known) vector do (vz = 0) (known) evaluate ($init_t = 1000 ) {* Initial simulated annealing temperature.*} vector do (vx = maxwell($init_t)) (attr mass>0) vector do (vy = maxwell($init_t)) (attr mass>0) vector do (vz = maxwell($init_t)) (attr mass>0) vector do (x=(random()-0.5)*20) (attr mass>0) vector do (y=(random()-0.5)*20) (attr mass>0) vector do (z=(random()-0.5)*20) (attr mass>0) !try bonds first flags exclude * include bond end constraints interaction (attr mass>0) (attr mass=0) interaction (attr mass>0) (attr mass>0) end !mini powell ! drop=1e5 ! nprint=1 ! tolg=1e-5 ! nstep=1000 !end flags exclude * include bond angle dihe cdihe impr vdw end !energy end !mini powell ! drop=1e5 ! nprint=1 ! tolg=1e-5 ! nstep=1000 !end evaluate ($kbon = 0.00005 ) {* Bonds. *} evaluate ($kang = 0.00005 ) {* Angles. *} evaluate ($timestep = 0.04) evaluate ($nstep = 100) !constraints ! interaction (all) (all) ! weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end !end !dynamics verlet ! nstep=5000 timestep=$timestep iasvel=current ! tcoupling=true tbath=$init_t nprint=50 iprfrq=0 !end while ($kbon < 0.01) loop stage1 evaluate ($kbon = min(0.25, $kbon * 1.25)) evaluate ($kang = $kbon) evaluate ($kimp = $kbon/10) noe scale * $knoe end !restraints dihed scale 0. end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 5e-4 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 5e-4 elec 0 end end dynamics verlet nstep=$nstep timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end end loop stage1 parameter {* Parameters for the repulsive energy term. *} nbonds repel=0.9 {* Initial value for repel - modified later. *} nbxmod=-3 {* Initial value for nbxmod - modified later. *} wmin=0.01 cutnb=4.5 ctonnb=2.99 ctofnb=3. tolerance=0.5 end end ! add vdw and slowly increase its weight parameter nbonds atom cutnb 100 tolerance 45 repel=1.2 rexp=2 irexp=2 rcon=1.0 nbxmod 4 end end flags exclude * include bond angle impr dihe cdihe vdw end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 0.002 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 0.002 elec 0 end end dynamics verlet nstep=500 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 0.005 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 0.005 elec 0 end end dynamics verlet nstep=500 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 0.01 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 0.01 elec 0 end end dynamics verlet nstep=500 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 0.5 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 0.5 elec 0 end end dynamics verlet nstep=500 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end !flags exclude * include bond angle end energy end mini powell drop=100 nprint=1 tolg=1e-5 nstep=10000 end constraints interaction (attr mass>0) (attr mass=0) weights bond $kbon angl $kang impr $kimp vdw 0.1 elec 0 end interaction (attr mass>0) (attr mass>0) weights bond $kbon angl $kang impr $kimp vdw 0.1 elec 0 end end mini powell drop=100 nprint=1 tolg=1e-5 nstep=10000 end write coord output=out.pdb end stop4. using the IVM (internal variable modules) for torsion angle dynamics and more
so far I have been using standard XPLOR protocols in XPLOR-NIH. I'd like to try the torsion angle dynamics, but have little idea of parameter settings. Would you have an example script, such as that described in Schwieters and Clore (2001) J. Magn. Reson., 152, 288-302, for protein G? Please contact Charles@Schwieters.org for that exact script. Examples of using the IVM can be found in multiple scripts located in the eginput directory of the Xplor-NIH distribution. In particular, see eginput/protG/anneal.inp5. I see errors like: Powell::step: irregular exit: Line search abandoned: gradient may be incorrect.
These messages are normal, and should not be of concern unless only a very small number of steps are being taken.6. Radius of gyration potential term
Using the radius of gyration restraint is similar to using an experimental term. First, you need to set up the restraint, and then you have to turn on its flag. To set up the restraint, use the COLLapse statement at the top of your script, near where you read in the NOEs: collapse assign (aSelection) 100.0 aTargetValue scale 1.0 end To turn it on, include COLL in your flags statement: flags exclude * include bond angle improper ... noe coll end You need to keep in mind a few things in order to set up the restraint properly: 1. The selections should not include any flexible regions. 2. The target value (in Angstroms) should be (2.2 * Nresidues^0.38) - 1 where Nresidues is the number of residues in the selection. 3. For anisotropic structures, you need to divide up your structure into several roughly spherical pieces and create a separate COLLapse ASSIgn statement for each. Other than those caveats, the Rgyr restraint is relatively bulletproof--it's not particularly sensitive to the force constant or whatever. And it doesn't affect sampling or convergence.7. DELPHIC torsion database of phi-psi angles
Hi Dr. Lecomte, Thanks for your email. The "raw" DELPHIC torsions code you're trying to use has been deprecated, in favor of using fitted Gaussians. To use the "raw" DELPHIC torsions, you'll need to change all your RAMA commands to XRAM. This includes every call to RAMA inside of the setup_longrange_4D_new.tbl script. Sorry for the incompatability--we're still cleaning up all the old code and examples. Note that you're almost certainly better off using the stuff in databases/torsions_gaussians or databases/torsions_quarts, since those approaches give *much* smoother forces on the atoms. See J Magn Resn 146 (2): 249-254 Oct 2000 . Please let us know if you find any more problems! --John Kuszewski8. DELPHIC torsion database of phi-psi angles: potential definition.
> calculations is negative. According with the original article E is > defined as > - - -k*log(Pi) where Pi is the probability, that I think should be > between 0 and > 1, so I don't understand how E can be negative. Do you know? > Thanks again, > Hugo The formulation for the DELPHIC torsion and DELPHIC position terms' potentials of mean force is E = -ln Pi, where Pi is the probability of being in bin i. Pi is now defined as (nExamples(i) / volume(i)) / overallDensity. This change was necessitated by some of the averaging I do to get a defined potential energy in unpopulated regions. If there are no examples in a particular bin, I start including that bin's neighbors along each axis until I reach a certain minimum number of examples. Then I divide by the total volume of the bins I just searched to get a "local density." In order for the units to work out correctly, I need to divide this local density by the overall density (totExamples / totVolume). The upshot is that regions of space that have greater-than-average density of examples now have negative energies, and regions with less-than-average density of examples now have positive energies.9. How do I determin the structure of a homo-dimer?
Add a NCS-style positional symmetry term to keep the subunits identical, and a distance symmetry term to maintain C2 symmetry. To a Python script, one would add # this assumes the two subunits have segids A and B: from distSymmTools import create_DistSymmPot, genDimerRestraints from selectTools import minResid, maxResid dSymm = create_DistSymmPot('dSymm', genDimerRestraints(segids=['A','B'], resids=range(minResid(), maxResid()+1,10))) potList.append(dSymm) # ``NCS'' term - keep dimer subunits identical from posDiffPotTools import create_PosDiffPot ncs = create_PosDiffPot("ncs","segid A","segid B") ncs.setScale(10) potList.append(ncs)10. dipolar couplings: the definition of the coefficients
> > Could you tell me what the exact meaning of the coefficients in SANI are? > I am confused about third coefficient which you call "rhombicity". Is this > "R" which is "Ar/Aa", or "Ar" itself? > this should answer your question: The SANI COEFficient statement takes three arguments: COEFficient11. dipolar couplings: how are force constants weighted between different experimentswhere the three real values are DFS, anisotropy, rhombicity. Their meaning becomes clear in the expression for the dipolar coupling shift: DFS + anisotropy*( (3*cos(theta)^2-1)+ rhombicity*(3/2)*sin(theta)^2*cos(2*phi) ) [note carefully the parentheses.]
> We are trying to incorporate multiple dipolar coupling constraints into our > structure calculations using xplor-nih. We have a sample input file for > xplor-nih that has a few force constants (CACO, NCO, HNC, CH) that appear to > be scaled relative to the N,NH force constant (for example, $k_sani_CACO = > 0.035*$ksani), but we are unclear about where these force constant estimates > come from, and how to estimate the missing ones (in particular, HNCA). Any > help in this regard would be most appreciated. > The force constants are based on the measurement error, and in the example you ask about, the dipolar couplings are all normalized relative to NH (which makes it easier to estimate the appropriate force constants). e.g. let us say the measurement error for the NH dipolar couplings is 1 Hz, then the final force constant should be around 1. Let us say that the error for the NC' coupling is around 0.5 Hz. The NC' couplings are 8.33 times smaller than the NH ones (from the bond lengths and gyromagnetic ratios), so when normalize to the NH couplings (by multiplying their values by 8.33) the error would be around 4 Hz. Since we minimize the square of the difference between observed and calculated, this would translate into a force constant that should be 1/16 that use for the NH couplings.12. Strange characters in output files or binary output files.
question: > I then ran the xplor and the .out, .pdb, and .psf files were > generated. I can view my protein in the vmd-xplor (.pdb). The only > problem is that when I try to see these files in a text editor this is > the message that I receive: > > [binary file or file with \000 character] It's probably due to bogus characters Xplor-NIH prints when it can't determine your username. This will be fixed in the next release. Until then you might fix your files using the following command: perl -i -pe 's/\000//g' file13. Xplor-NIH for similar computers.
If you think that Xplor-NIH should run on your computer, but it gives a message like: xplor not configured for platform: $ARCH Try adding a line to the file arch/equivList of the form OARCH ARCH where OARCH is the architecture string given in the distribution and ARCH is the string which Xplor-NIH claims is not supported.14. What are random number seeds?
> I have a quick question to ask you about the random number > generation SEED in XPLOR-NIH. The scripts supplied in the eginputs use > either $seed=778, or $seed=65748309 for the initial velocities. Are > these differences related to the architecture of the computer used for > calculations? I'm running Mandrake 9.0 linux, and have had to adjust > things like the maximum for random number generation in other types of > programs (I typically use values for this of 2144563822.0), and use > seed values of say 82364 (which is actually what I use for CNS > calculations). The exact value of the seed shouldn't matter too much- but it shouldn't be too large- because the XPLOR interface stores the seed as a floating point number, strange things happen it the seed gets larger than about 10^8. > Will altering the SEED change things much? Or will it > just produce a slightly different set of results. The value of the seed controls the exact sequence of pseudo-random numbers used for things like setting initial random velocities. Thus, changing the seed will change the details of a particular structure. However, the set of final structures should be relatively insensitive to the seed value. If the set of results does depend sensitively on seed, it usually means that the optimization protocol needs some further work.15. why do I get the error: %ASSFIL-ERR: no free unit available?
You are probably redirecting print or display output to a file. When you do this, and you also want some output to come out stdout, you must perform two steps: close the file, and redirect output to OUTPUT. Here's an example: set print=noe.out end print noe thresh=0.5 end close noe.out end set print=OUTPUT end If you do not both close the file and redirect output back to stdout, you will run out of files if you run many structures. Another effect of not redirecting print or display output back to OUTPUT is that subsequent output to stdout will not occur. Rather the data will be written to a file named fort.# (the filename is system dependent).16. Why do I get the error %COPYST-ERR: ST2MAX too small. Check input file?
This is usually due to lines which are too long. The maximum line length in the XPLOR interface of Xplor-NIH is 132 characters. You can work around the error by inserting carriage returns in the offending line, such that it is no longer too long.17. Why do I get the error cannot restore segment prot after reloc: Permission denied
This is due to a conflict with Security Enhanced Linux (SELinux) as configured in some distributions. You can get Xplor-NIH running in one of two ways: * Change the default security context for Xplor-NIH by issuing the command: find . -name \*.so -exec chcon -t texrel_shlib_t {} \; in the top level Xplor-NIH directory. or * Disable SELinux altogether by setting the line SELINUX=disabled in your /etc/sysconfig/selinux file. Then reboot.18. Are Intel-based Macs supported?
Yes. By the Darwin_8_x86 packages on the download site.19. Can Xplor-NIH 2.24 (and maybe earlier) run on Maxc OS X 10.6?
Yes. In the xplor-nih distribution directory, please execute these two commands: echo "Darwin_8_x86 Darwin_9_x86 Darwin_10_x86" >> arch/equivList rm bin.Darwin_8_x86/libgcc_s.1.dylib20. Why doesn't Xplor-NIH run on fedora core 5?
Applies for Xplor-NIH versions prior to 2.15: This can be worked around by editing bin/xplor.in in the distribution directory and removing the following lines: if [ $arch = "Linux_2.4_i686" ]; then # # kludge for Redhat kernels with back-ported thread library. # LD_ASSUME_KERNEL="2.4.19" exported="$exported LD_ASSUME_KERNEL" fi This workaround also seems to help for newer versions of the Suse, and Gentoo distributions.21. does Xplor-NIH support parallel computer architectures?
Scripts generating multiple structures can be conveniently parallelized using the -parallel command-line switch. An example of this use is shown on page 43 of the slides at http://bit.niddk.nih.gov/xplor-nih/nih/class08Dec2006.pdf Also, shared memory parallelism can be employed when performing refinement on an ensemble of structures. Please enquire for more details. Please see http://bit.niddk.nih.gov/xplor-nih/parallel.txt (or parallel.txt in the Xplor-NIH distribution directory) for details.22. How do I run Xplor-NIH on a cluster using the PBS queuing system?
An example PBS script can be found at http://bit.niddk.nih.gov/xplor-nih/nih/xplor.pbs