Hi, Dallas: I added this to the ffoplsaa.rtp
[ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3 SI O SI dih_PDM_chi1_C_SI_O_SI SI O SI CH3 dih_PDM_chi1_SI_O_SI_C O SI O SI dih_PDM_chi1_O_SI_O_SI The format is the same with other entries. Do you guys think anything wrong with it? Also what does it mean by the error message: 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: ------------------------------------------------------- what is "Source code file: resall.c, line: 289" It seems the problem comes from here. Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren <dallas.war...@pharm.monash.edu.au> wrote: > Check consistency with other entries around it, easy way to check to see that > you have the right format. > > What did you edit the file with? > > 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: Thursday, 30 April 2009 9:07 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> This is the new entry I added to the rtp file. >> >> [ PDM ] >> >> >> [ atoms ] >> SI SI 0.300 1 >> CH3 opls_069 0.000 1 >> O opls_108 -0.300 1 >> >> >> [ bonds ] >> SI O 0.190 158805.0 >> SI CH3 0.164 293160.0 >> >> >> [ dihedrals ] >> CH3 SI O SI 3.77 3 0 >> SI O SI CH3 3.77 3 0 >> O SI O SI 3.77 3 0 >> >> >> On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul >> <jalem...@vt.edu> wrote: >> > >> > >> > Yanmei Song wrote: >> > >> >> ------------------------------------------------------- >> >> Program pdb2gmx, VERSION 3.3.3 >> >> Source code file: resall.c, line: 289 >> >> >> >> Fatal error: >> >> in .rtp file at line: >> >> >> >> >> >> ------------------------------------------------------- >> > >> > Well that's not a terribly helpful error message, is it? :) >> > >> > There is probably something wrong with the .rtp entry you >> created. If you >> > can post that, perhaps someone can spot it. >> > >> > -Justin >> > >> > -- >> > ======================================== >> > >> > 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-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