Dear Justin and Dallas: Thank you for your help earlier.
I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 6 Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp ------------------------------------------------------- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: ------------------------------------------------------- And also my pdb file: ATOM 1 Si1 PDM A 1 3.796 2.499 -0.834 1.00 0.00 ATOM 2 O2 PDM A 1 4.661 1.181 -0.025 1.00 0.00 ATOM 3 Si4 PDM A 1 4.896 -0.181 1.082 1.00 0.00 ATOM 4 O6 PDM A 1 3.686 -1.442 0.846 1.00 0.00 ATOM 5 Si7 PDM A 1 2.036 -2.061 0.903 1.00 0.00 ATOM 6 O8 PDM A 1 2.038 -3.727 0.331 1.00 0.00 ATOM 7 Si9 PDM A 1 1.180 -5.229 0.010 1.00 0.00 ATOM 8 O10 PDM A 1 2.299 -6.424 -0.637 1.00 0.00 ATOM 9 Si16 PDM A 1 3.364 -7.030 -1.904 1.00 0.00 ATOM 10 O17 PDM A 1 4.537 -5.799 -2.367 1.00 0.00 ATOM 11 Si18 PDM A 1 5.956 -5.364 -3.320 1.00 0.00 ATOM 12 O22 PDM A 1 6.259 -3.637 -3.183 1.00 0.00 ATOM 13 Si24 PDM A 1 5.682 -1.997 -3.451 1.00 0.00 ATOM 14 O26 PDM A 1 6.879 -0.842 -2.885 1.00 0.00 ATOM 15 Si28 PDM A 1 8.515 -0.209 -2.996 1.00 0.00 ATOM 16 O29 PDM A 1 8.808 0.346 -4.640 1.00 0.00 ATOM 17 Si30 PDM A 1 9.879 1.063 -5.838 1.00 0.00 ATOM 18 C34 PDM A 1 9.731 -1.561 -2.566 1.00 0.00 ATOM 19 C36 PDM A 1 8.720 1.221 -1.809 1.00 0.00 ATOM 20 C38 PDM A 1 6.585 -0.914 0.764 1.00 0.00 ATOM 21 C40 PDM A 1 4.835 0.406 2.852 1.00 0.00 ATOM 22 C42 PDM A 1 5.391 -1.730 -5.278 1.00 0.00 ATOM 23 C44 PDM A 1 4.080 -1.754 -2.529 1.00 0.00 ATOM 24 C46 PDM A 1 7.441 -6.315 -2.701 1.00 0.00 ATOM 25 C48 PDM A 1 5.652 -5.789 -5.115 1.00 0.00 ATOM 26 C50 PDM A 1 2.345 -7.495 -3.401 1.00 0.00 ATOM 27 C52 PDM A 1 4.259 -8.545 -1.272 1.00 0.00 ATOM 28 C54 PDM A 1 0.462 -5.872 1.612 1.00 0.00 ATOM 29 C56 PDM A 1 -0.201 -4.930 -1.214 1.00 0.00 ATOM 30 C58 PDM A 1 1.428 -2.016 2.670 1.00 0.00 ATOM 31 C60 PDM A 1 0.900 -1.032 -0.161 1.00 0.00 ATOM 32 O62 PDM A 1 3.063 3.615 0.320 1.00 0.00 ATOM 33 Si63 PDM A 1 1.897 4.001 1.587 1.00 0.00 ATOM 34 O64 PDM A 1 2.116 5.675 2.077 1.00 0.00 ATOM 35 Si68 PDM A 1 3.148 6.934 2.744 1.00 0.00 ATOM 36 C69 PDM A 1 3.682 6.458 4.471 1.00 0.00 ATOM 37 C72 PDM A 1 5.023 3.440 -1.884 1.00 0.00 ATOM 38 C74 PDM A 1 2.464 1.816 -1.948 1.00 0.00 ATOM 39 C76 PDM A 1 0.164 3.775 0.923 1.00 0.00 ATOM 40 C78 PDM A 1 2.137 2.886 3.063 1.00 0.00 ATOM 41 C80 PDM A 1 2.202 8.545 2.805 1.00 0.00 ATOM 42 Si84 PDM A 1 4.922 7.171 1.466 1.00 0.00 ATOM 43 C84 PDM A 1 8.984 1.182 -7.476 1.00 0.00 ATOM 44 C86 PDM A 1 10.387 2.774 -5.280 1.00 0.00 ATOM 45 C88 PDM A 1 11.401 -0.004 -6.037 1.00 0.00 TER Do you have any idea what I did wrong? It seems the GROMACS doesn't give the wrong line by Fatal error: in .rtp file at line: ------------------------------------------------------- Thank you so much for your help in advance! On Tue, Apr 28, 2009 at 4:38 PM, Dallas B. Warren <dallas.war...@pharm.monash.edu.au> wrote: > That is correct. Fact you can't edit the .rtp file is based on your local > computer system permissions. Normally, best idea is to make your own changes > to a local copy, and use that. > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -----Original Message----- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Wednesday, 29 April 2009 9:24 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> Dear Dallas: >> >> Thanks for your response. It consists of many repeating units. Do you >> mean I can write the rtp entry for one repeating unit and give it a >> residue name. After that I need to insert this into the force field >> rtp file, right? How can I do that? It seems I can not change the rtp >> file. Thanks. >> >> On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren >> <dallas.war...@pharm.monash.edu.au> wrote: >> > If it is a repeating unit, then you can build a .rtp entry >> then use it as you would for a protein. >> > >> > Catch ya, >> > >> > Dr. Dallas Warren >> > Department of Pharmaceutical Biology and Pharmacology >> > Pharmacy and Pharmaceutical Sciences, Monash University >> > 381 Royal Parade, Parkville VIC 3010 >> > dallas.war...@pharm.monash.edu.au >> > +61 3 9903 9167 >> > --------------------------------- >> > When the only tool you own is a hammer, every problem >> begins to resemble a nail. >> > >> >> -----Original Message----- >> >> From: gmx-users-boun...@gromacs.org >> >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> >> Sent: Wednesday, 29 April 2009 8:59 AM >> >> To: jalem...@vt.edu; Discussion list for GROMACS users >> >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> >> >> Dear Justin: >> >> >> >> Do you have any suggestions on how I can get the itp and >> gro file for >> >> a very long polymer molecules (for example 500 united-atoms), which >> >> only consists of Si, O and C atom. I can use PRODRG to generate a >> >> short chain. But PRODRG has limitation of atom numbers in >> a molecule, >> >> probably less than 300. So any ideas for building up a long chain >> >> based on the short chain? By the way, I already have the >> force field >> >> parameters. >> >> >> >> Thanks a lot! >> >> >> >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul >> >> <jalem...@vt.edu> wrote: >> >> > >> >> > >> >> > Yanmei Song wrote: >> >> >> >> >> >> Dear All users: >> >> >> >> >> >> I was trying to set up a long chain polymer system. I got the >> >> >> following PDB file from WebLab. How can I make changes to >> >> the file in >> >> >> order to make it as a GROMACS input pdb file. Then I can >> >> use pdb2gmx >> >> >> to get the gro, itp and top file. >> >> >> >> >> >> When I perform the pdb2gmx command, I got the error message: >> >> >> >> >> >> Residue 'MOL' not found in residue topology database >> >> >> >> >> > >> >> > You can't expect pdb2gmx to be magic. A simple search of >> >> the list archives >> >> > and wiki will turn up the following: >> >> > >> >> > >> >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not >> > _found_in_residue_topology_database >> >> > >> >> > -Justin >> >> > >> >> >> Thank you in advance! >> >> >> >> >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain >> >> Standard Time 2009 >> >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 >> 1.00 0.00 >> >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 >> 1.00 0.00 >> >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 >> 1.00 0.00 >> >> >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 >> 1.00 0.00 >> >> >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 >> 1.00 0.00 >> >> >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 >> 1.00 0.00 >> >> >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 >> 1.00 0.00 >> >> >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 >> 1.00 0.00 >> >> >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 >> 1.00 0.00 >> >> >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 >> 1.00 0.00 >> >> >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 >> 1.00 0.00 >> >> >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 >> 1.00 0.00 >> >> >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 >> 1.00 0.00 >> >> >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 >> 1.00 0.00 >> >> >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 >> 1.00 0.00 >> >> >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 >> 1.00 0.00 >> >> >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 >> 1.00 0.00 >> >> >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 >> 1.00 0.00 >> >> >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 >> 1.00 0.00 >> >> >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 >> 1.00 0.00 >> >> >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 >> 1.00 0.00 >> >> >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 >> 1.00 0.00 >> >> >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 >> 1.00 0.00 >> >> >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 >> 1.00 0.00 >> >> >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 >> 1.00 0.00 >> >> >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 >> 1.00 0.00 >> >> >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 >> 1.00 0.00 >> >> >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 >> 1.00 0.00 >> >> >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 >> 1.00 0.00 >> >> >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 >> 1.00 0.00 >> >> >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 >> 1.00 0.00 >> >> >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 >> 1.00 0.00 >> >> >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 >> 1.00 0.00 >> >> >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 >> 1.00 0.00 >> >> >> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 >> 1.00 0.00 >> >> >> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 >> 1.00 0.00 >> >> >> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 >> 1.00 0.00 >> >> >> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 >> 1.00 0.00 >> >> >> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 >> 1.00 0.00 >> >> >> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 >> 1.00 0.00 >> >> >> ATOM 41 C80 MOL A 1 2.186 8.538 2.814 >> 1.00 0.00 >> >> >> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 >> 1.00 0.00 >> >> >> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 >> 1.00 0.00 >> >> >> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 >> 1.00 0.00 >> >> >> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 >> 1.00 0.00 >> >> >> TER >> >> >> >> >> >> >> >> > >> >> > -- >> >> > ======================================== >> >> > >> >> > Justin A. Lemkul >> >> > Ph.D. Candidate >> >> > 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 gmx-us...@gromacs.org >> >> > 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 gmx-users-requ...@gromacs.org. >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > >> >> >> >> >> >> >> >> -- >> >> Yanmei Song >> >> Department of Chemical Engineering >> >> ASU >> >> _______________________________________________ >> >> gmx-users mailing list gmx-us...@gromacs.org >> >> 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 gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > _______________________________________________ >> > gmx-users mailing list gmx-us...@gromacs.org >> > 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 gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >> >> >> -- >> Yanmei Song >> Department of Chemical Engineering >> ASU >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
