Well some of the problems in the log relate to unresolved exceptions processing the ligands, those ligands are skipped. But I should probably just test the receptors seperate from the workflow and merged ligands. I will check this list provided by Tsjerk. Possibly the numbering is off. Anyway its the structures that need a little work. 6. there should be no atoms in residues that are not listed in the building block entry, except possibly for hydrogen atoms, which can be stripped using the -ignh flag Currently I use -ignh, should I see what happens when I remove this option? Will that reveal innappropriate atoms that I should remove? On Sun, Jan 10, 2010 at 9:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > On 1/10/10 9:47 PM, Jack Shultz wrote: > >> Thanks Justin, >> I went back to the original pdb files. These were conformations of the >> same protein derived from molecular dynamics simulations performed by >> Andrey. >> What I intially attempted was preping the structures using tleap, hoping >> to paint in missing atoms for residues. Then use this to replace >> > > Well, it seems that you may be hoping for too much :) Your log file shows > a whole bunch of failures that look to be related to some early processing > of your structure, and other warnings about close contacts detected in > tleap. > > I think you may need to start with an actual intact structure, or else coax > your preparation steps to make this happen. I am not too familiar with > tleap and sleap, do they magically fix missing atoms? > > -Justin > > non-standard residues >> sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\ >> \ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ >> \ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ >> CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed >> s/CYS\ /CYN\ /g > protein2.pdb >> Then fixed the nterminal residue name. Finally replaced all CYS to CYS2 >> I went back and did the same thing except for tleap. It pdb2gmx seems to >> process these files without needing the tleap step. >> Still I see some of the same lincs errors. >> rms 10.669050, max 173.182678 (between atoms 1857 and 1859) >> rms 10.669803, max 173.177811 (between atoms 1857 and 1859) >> rms 10.670179, max 173.175400 (between atoms 1857 and 1859) >> rms 10.670368, max 173.174149 (between atoms 1857 and 1859) >> rms 10.670460, max 173.173553 (between atoms 1857 and 1859) >> rms 10.670508, max 173.173141 (between atoms 1857 and 1859) >> rms 10.670531, max 173.173035 (between atoms 1857 and 1859) >> rms 10.670543, max 173.172958 (between atoms 1857 and 1859) >> rms 10.670549, max 173.172928 (between atoms 1857 and 1859) >> rms 10.670552, max 173.172913 (between atoms 1857 and 1859) >> rms 10.670554, max 173.172913 (between atoms 1857 and 1859) >> rms 10.670554, max 173.172913 (between atoms 1857 and 1859) >> ATOM 1857 CA HIE 120 43.362 28.084 25.727 1.00 0.00 >> ATOM 1858 HA HIE 120 43.677 27.135 25.748 1.00 0.00 >> ATOM 1859 CB HIE 120 42.112 28.226 24.788 1.00 0.00 >> also this atom consistently has a very high Fmax >> Step= 3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12, >> atom= 19392 >> Step= 4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12, >> atom= 19392 >> Step= 5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12, >> atom= 19392 >> Step= 6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12, >> atom= 19392 >> Step= 7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12, >> atom= 19392 >> Its not clear to me what we should do to correct this structures...maybe >> Andrey has some input. >> http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt >> On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 1/10/10 5:18 PM, Jack Shultz wrote: >> >> I am trying to get this workflow opperational. However, my >> systems are >> getting unstable. I have preped two mdp files: 1) one for >> restrained 2) >> unrestrained. LINCS errors appear for restrained and >> unrestrained has >> infinite energy appearing. >> http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_ >> >> <http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt> >> __ >> >> >> This log file shows several "long bond" warnings, which may be the >> root of your problem. See here: >> >> >> http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms >> >> Since your minimization is failing immediately, there is something >> physically unreasonable about your structure, such that EM cannot >> resolve the problem. Note, too, that one of the long bond warnings >> pertained to atom 1668, which is the location of the first LINCS >> warning. Coincidence? Not likely. Re-examine the starting >> structure and figure out if anything is missing or poorly >> reconstructed (e.g., from initially missing atoms). >> >> >> This is where I get the LINCS Warnings >> Step -1, time -0.001 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.461520, max 14.428611 (between atoms 1668 and 1669) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+04 >> Number of steps = 100 >> Warning: 1-4 interaction between 1658 and 1672 at distance 2.655 >> which >> is larger than the 1-4 table size 2.400 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> Step= 0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11, >> atom= 3292 >> Step 1, time 0.001 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.680509, max 22.293625 (between atoms 1668 and 1670) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> What is a reasonable increase in table-extension. Is this a >> mis-leading >> suggestion? >> >> >> You should not adjust the table-extension. The other part of the >> error message is what you need to pay attention to ("your system is >> exploding"). >> >> -Justin >> >> Here is the log from the unrestrained minimization. >> http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_ >> >> <http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt> >> Here is a zip archive containing the working directory for this >> minimization. Its about 428 kb >> >> http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip >> >> -- >> Jack >> >> http://drugdiscoveryathome.com <http://drugdiscoveryathome.com/> >> http://hydrogenathome.org <http://hydrogenathome.org/> >> >> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org
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