Hi, Justin: Thank you so much for your nice help. I will work on that according to your suggestions.
On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yanmei Song wrote: >> >> 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. > > That is the line of code that is spotting a problem. > > I think the issue is that, in your original .pdb file, you have dozens of > atoms in your polymer chain, all labeled as residue 1. What your .rtp entry > says is that a single PDM should contain only three atoms. Since what you > are trying to do is make a building block, you will need to do several > things: > > 1. Re-number your .pdb file so that multiple monomers are apparent. > 2. Use the + and - characters to indicate connectivity to the next residue > and previous residue, respectively. > 3. Create separate .rtp entries for terminal groups, as I suggested > previously, so that termini are handled correctly (since the -n.tdb and > -c.tdb files cannot be used for non-protein). > > See the amino acid entries for examples on how to use + and - appropriately, > or the list archive for examples provided by other users for other polymers > (polyethylene is especially common), for example: > > http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html > > -Justin > >> >> 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 >>> >> >> >> > > -- > ======================================== > > 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
