<div>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.<br>
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<div>6. there should be no atoms in residues that are not listed in the<br>building block entry, except possibly for hydrogen atoms, which can be<br>stripped using the -ignh flag</div>
<div>Currently I use -ignh, should I see what happens when I remove this option? Will that reveal innappropriate atoms that I should remove?<br></div>
<div class="gmail_quote">On Sun, Jan 10, 2010 at 9:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="im"><br><br>On 1/10/10 9:47 PM, Jack Shultz wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks Justin,<br>I went back to the original pdb files. These were conformations of the<br>same protein derived from molecular dynamics simulations performed by<br>
Andrey.<br>What I intially attempted was preping the structures using tleap, hoping<br>to paint in missing atoms for residues. Then use this to replace<br></blockquote><br></div>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.<br>
<br>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?<br><br>-Justin<br>
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<div class="h5">non-standard residues<br>sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\<br>\ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\<br>\ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\<br>
CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed<br>s/CYS\ /CYN\ /g > protein2.pdb<br>Then fixed the nterminal residue name. Finally replaced all CYS to CYS2<br>I went back and did the same thing except for tleap. It pdb2gmx seems to<br>
process these files without needing the tleap step.<br>Still I see some of the same lincs errors.<br>rms 10.669050, max 173.182678 (between atoms 1857 and 1859)<br>rms 10.669803, max 173.177811 (between atoms 1857 and 1859)<br>
rms 10.670179, max 173.175400 (between atoms 1857 and 1859)<br>rms 10.670368, max 173.174149 (between atoms 1857 and 1859)<br>rms 10.670460, max 173.173553 (between atoms 1857 and 1859)<br>rms 10.670508, max 173.173141 (between atoms 1857 and 1859)<br>
rms 10.670531, max 173.173035 (between atoms 1857 and 1859)<br>rms 10.670543, max 173.172958 (between atoms 1857 and 1859)<br>rms 10.670549, max 173.172928 (between atoms 1857 and 1859)<br>rms 10.670552, max 173.172913 (between atoms 1857 and 1859)<br>
rms 10.670554, max 173.172913 (between atoms 1857 and 1859)<br>rms 10.670554, max 173.172913 (between atoms 1857 and 1859)<br>ATOM 1857 CA HIE 120 43.362 28.084 25.727 1.00 0.00<br>ATOM 1858 HA HIE 120 43.677 27.135 25.748 1.00 0.00<br>
ATOM 1859 CB HIE 120 42.112 28.226 24.788 1.00 0.00<br>also this atom consistently has a very high Fmax<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12,<br>atom= 19392<br>Step= 4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12,<br>
atom= 19392<br>Step= 5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12,<br>atom= 19392<br>Step= 6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12,<br>atom= 19392<br>Step= 7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12,<br>
atom= 19392<br>Step= 8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12,<br>atom= 19392<br>Step= 9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12,<br>atom= 19392<br>Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12,<br>
atom= 19392<br>Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12,<br>atom= 19392<br>Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12,<br>atom= 19392<br>Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12,<br>
atom= 19392<br>Its not clear to me what we should do to correct this structures...maybe<br>Andrey has some input.<br><a href="http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt" target="_blank">http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt</a><br>
On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div></div>
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<div class="h5"><mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> On 1/10/10 5:18 PM, Jack Shultz wrote:<br><br> I am trying to get this workflow opperational. However, my<br>
systems are<br> getting unstable. I have preped two mdp files: 1) one for<br> restrained 2)<br> unrestrained. LINCS errors appear for restrained and<br> unrestrained has<br> infinite energy appearing.<br>
<a href="http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_" target="_blank">http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_</a><br><br> <<a href="http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt" target="_blank">http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt</a>><br>
__<br><br><br> This log file shows several "long bond" warnings, which may be the<br> root of your problem. See here:<br><br> <a href="http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms" target="_blank">http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms</a><br>
<br> Since your minimization is failing immediately, there is something<br> physically unreasonable about your structure, such that EM cannot<br> resolve the problem. Note, too, that one of the long bond warnings<br>
pertained to atom 1668, which is the location of the first LINCS<br> warning. Coincidence? Not likely. Re-examine the starting<br> structure and figure out if anything is missing or poorly<br> reconstructed (e.g., from initially missing atoms).<br>
<br><br> This is where I get the LINCS Warnings<br> Step -1, time -0.001 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> rms 0.461520, max 14.428611 (between atoms 1668 and 1669)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+04<br> Number of steps = 100<br>
Warning: 1-4 interaction between 1658 and 1672 at distance 2.655<br> which<br> is larger than the 1-4 table size 2.400 nm<br> These are ignored for the rest of the simulation<br> This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br> or with user tables increase the table size<br> Step= 0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11,<br> atom= 3292<br>
Step 1, time 0.001 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> rms 0.680509, max 22.293625 (between atoms 1668 and 1670)<br> bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> What is a reasonable increase in table-extension. Is this a<br> mis-leading<br> suggestion?<br><br><br> You should not adjust the table-extension. The other part of the<br>
error message is what you need to pay attention to ("your system is<br> exploding").<br><br> -Justin<br><br> Here is the log from the unrestrained minimization.<br> <a href="http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_" target="_blank">http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_</a><br>
<br> <<a href="http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt" target="_blank">http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt</a>><br> Here is a zip archive containing the working directory for this<br>
minimization. Its about 428 kb<br> <a href="http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip" target="_blank">http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip</a><br>
<br> --<br> Jack<br><br></div></div> <a href="http://drugdiscoveryathome.com/" target="_blank">http://drugdiscoveryathome.com</a> <<a href="http://drugdiscoveryathome.com/" target="_blank">http://drugdiscoveryathome.com/</a>><br>
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<div class="im"><br><br><br> --<br> ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br>
Virginia Tech<br> Blacksburg, VA<br></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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