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-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 > _______________________________________________ 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