<div>Thanks Justin,</div>
<div> </div>
<div>I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. </div>
<div> </div>
<div>What I intially attempted was preping the structures using tleap, hoping to paint in missing atoms for residues. Then use this to replace non-standard residues</div>
<div>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</div>
<div> </div>
<div>Then fixed the nterminal residue name. Finally replaced all CYS to CYS2</div>
<div> </div>
<div>I went back and did the same thing except for tleap. It pdb2gmx seems to process these files without needing the tleap step.</div>
<div>Still I see some of the same lincs errors. </div>
<div> </div>
<div>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>
</div>
<div>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></div>
<div>also this atom consistently has a very high Fmax</div>
<div>Step= 3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12, atom= 19392<br>Step= 4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12, atom= 19392<br>Step= 5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12, atom= 19392<br>
Step= 6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12, atom= 19392<br>Step= 7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12, atom= 19392<br>Step= 8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12, atom= 19392<br>
Step= 9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12, atom= 19392<br>Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12, atom= 19392<br>Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12, atom= 19392<br>
Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12, atom= 19392<br>Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12, atom= 19392</div>
<div> </div>
<div>Its not clear to me what we should do to correct this structures...maybe Andrey has some input.<br><a href="http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt">http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt</a><br>
</div>
<div class="gmail_quote">On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>On 1/10/10 5:18 PM, Jack Shultz wrote:<br></div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">I am trying to get this workflow opperational. However, my systems are<br>getting unstable. I have preped two mdp files: 1) one for restrained 2)<br>unrestrained. LINCS errors appear for restrained and unrestrained has<br>
infinite energy appearing.<br></div><a href="http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_" target="_blank">http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_</a>
<div class="im"><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></div></blockquote><br>
This log file shows several "long bond" warnings, which may be the 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 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).
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">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 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 mis-leading<br>
suggestion?<br></blockquote><br></div>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").<br><br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">Here is the log from the unrestrained minimization.<br></div><a href="http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_" target="_blank">http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_</a>
<div class="im"><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><a href="http://drugdiscoveryathome.com/" target="_blank">http://drugdiscoveryathome.com</a><br><a href="http://hydrogenathome.org/" target="_blank">http://hydrogenathome.org</a><br><br></div></blockquote>
<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><br>========================================<br><font color="#888888">-- <br>
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