Dear Justin and gmx-users: Thank you for your answer, Justin.
Since I corrected error related to "blank" in the input files (pdb and etc.), it has never given me "segmentation fault." So... this problem is not related to this one anyway. Now, I will try to correct others by following your suggestion. After trying, I will contact you again... :) Thank you again!! Sincerely yours, C Kim On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul <[email protected]> wrote: > > > Chansoo Kim wrote: > >> Dear Justin: >> >> >> Thank you for your reply. >> I was too urgent, so I did not clarify my questions. >> Sorry about that. >> >> I totally understand how topology files (tdb, hdb, and etc..) work, but I >> do not clearly understand chemical reaction, which I have to define in those >> files... >> >> > No chemical reactions occur :) See comments embedded below > > > >> [Situation] >> I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force >> field... >> >> [Topology files and etc] >> (1) rtp file >> >> [ Eth ] >> [ atoms ] >> C1 opls_136 -0.120 1 >> H11 opls_140 0.060 1 >> H12 opls_140 0.060 1 >> C2 opls_136 -0.120 2 >> H21 opls_140 0.060 2 >> H22 opls_140 0.060 2 >> [ bonds ] >> C1 H11 >> C1 H12 >> C1 C2 >> C2 H21 >> C2 H22 >> C2 +C1 >> >> >> (2) hdb file >> Eth 2 >> 2 6 H1 C1 C2 +C1 >> 2 6 H2 C2 C1 -C2 >> >> >> (3) -c.tdb file >> >> [ Eth ] >> [ replace ] >> C1 opls_135 12.011 -0.18 >> [ add ] >> 3 4 H1 C1 C2 >> opls_140 1.008 0.06 >> [ delete ] >> H21 >> H22 >> >> >> (4) -n.tdb file >> >> [ Eth ] >> [ replace ] >> C2 opls_135 12.011 -0.18 >> [ add ] >> 3 4 H2 C2 C1 >> opls_140 1.008 0.06 >> [ delete ] >> H21 >> H22 >> >> > Note that the message you referenced in your first post (which provided you > with this .rtp entry) resulted in a segmentation fault, therefore indicating > that it probably won't work. > > >> (5) input pdb file >> >> ATOM 1 C1 Eth 1 1.000 1.540 0.000 >> >> ATOM 2 C2 Eth 1 2.456 2.041 0.000 >> ATOM 3 C1 Eth 2 2.456 3.581 0.000 >> ATOM 4 C2 Eth 2 3.912 4.083 0.000 >> ATOM 5 C1 Eth 3 3.912 5.623 0.000 >> ATOM 6 C2 Eth 3 5.368 6.124 0.000 >> END >> >> >> [Error] >> When I did run the pdb2gmx, I got the following error. >> "Atom -C not found in residue PEth1 while adding hydrogens" >> >> [Question #1 and #2] >> Therefore, what I should define more...? >> What does the "+" and "-" mean here? >> > > + means next residue, - means previous. > > >> >> [If...] >> If I change the hdb file as follows, >> >> Eth 2 >> 2 6 H1 C1 C2 C1 >> 2 6 H2 C2 C1 C2 >> >> >> After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did >> NOT work...). >> And those positions are all (0, 0, 0). >> >> > Right, because H positioning in a polymer chain may depend on previous (-) > or subsequent (+) residues, so the code doesn't know where to put them. > > > Following is the results, >> >> LE Giving Russians Opium May Alter Current Situation >> MODEL 1 >> ATOM 1 C1 PEt 1 1.000 0.000 0.000 1.00 0.00 >> ATOM 2 H11 PEt 1 0.000 0.000 0.000 1.00 0.00 >> ATOM 3 H12 PEt 1 0.000 0.000 0.000 1.00 0.00 >> ATOM 4 C2 PEt 1 2.450 6.000 1.000 1.00 0.00 >> ATOM 5 H21 PEt 1 0.000 0.000 0.000 1.00 0.00 >> ATOM 6 H22 PEt 1 0.000 0.000 0.000 1.00 0.00 >> ATOM 7 C1 PEt 2 2.450 6.000 1.000 1.00 0.00 >> ATOM 8 H11 PEt 2 0.000 0.000 0.000 1.00 0.00 >> ATOM 9 H12 PEt 2 0.000 0.000 0.000 1.00 0.00 >> ATOM 10 C2 PEt 2 3.910 2.000 3.000 1.00 0.00 >> ATOM 11 H21 PEt 2 0.000 0.000 0.000 1.00 0.00 >> ATOM 12 H22 PEt 2 0.000 0.000 0.000 1.00 0.00 >> ATOM 13 C1 PEt 3 3.910 2.000 3.000 1.00 0.00 >> ATOM 14 H11 PEt 3 0.000 0.000 0.000 1.00 0.00 >> ATOM 15 H12 PEt 3 0.000 0.000 0.000 1.00 0.00 >> ATOM 16 C2 PEt 3 5.360 8.000 4.000 1.00 0.00 >> ATOM 17 H21 PEt 3 0.000 0.000 0.000 1.00 0.00 >> ATOM 18 H22 PEt 3 0.000 0.000 0.000 1.00 0.00 >> TER >> ENDMDL >> >> [Question #3 from If... section ] >> I guess that I have to change hdb and tdb files. >> Would you please give some guide on that...? >> >> > Knowing that many people have tried to define PE with .tdb entries (and I > think success is limited), I would suggest the following. Define distinct > .rtp entries for the caps of your chain. Don't bother with -n.tdb and > -c.tdb; I don't know how well the Gromacs code handles non-protein termini > (maybe it works, but it seems to give fits for polymers). The .rtp entry > for PE you've shown above seems reasonable enough for a PE monomer within > the chain, but may require some tweaking (since I've never tried, I don't > know). > > -Justin > > Thank you for your care! >> >> >> Sincerely yours, >> >> C Kim >> >> On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Chansoo Kim wrote: >> >> Dear Dr. Benkova and others: >> >> >> I am C. Kim and trying to simulation polymer system. >> >> Since I guessed that polyethylene (PE) is a simple system, it >> could be not that hard to simulate it in Gromacs. >> Trying to do, I have read Dr. Benkova's articles in gmx-users >> mailing list to tackle my problems. >> Sorry to say, I could not solve problems, so I am asking your help! >> >> Actually I have used your files written in followings, >> >> http://www.mail-archive.com/[email protected]/msg12204.html >> >> [Q1] >> After getting the result from the pdb2gmx, I could not see any >> H-atoms in my system. >> All the H-atoms have 0, 0, 0 positions! >> Therefore, my question is >> how I should define hdb? >> >> >> The .hdb file format is explained in the manual. >> >> >> >> [Q2] >> When I use -C2, and +C1 in hdb file, I always meet error. >> >> >> What is the error? >> >> -Justin >> >> Is there any other things to add to the ffopls*.* files...? >> >> Thank you for your care! >> >> >> Sincerely >> C. Kim >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://www.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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> 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 [email protected] >> <mailto:[email protected]> >> http://www.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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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 [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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