Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message:
Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/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 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp ------------------------------------------------------- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: ------------------------------------------------------- My new residue added to ffoplass.rtp is: [ PDM ] ; designation arbitrary, C1 and C2 is -CH3 [ atoms ] SI1 SI 0.300 1 C1 opls_069 0.000 1 C2 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue ("beginning" of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDMB ] [ atoms ] C1 opls_069 0.000 1 SI1 SI 0.300 1 C2 opls_069 0.000 1 C3 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1 O1 O1 +SI1 ; Terminal PE residue ("end" of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDME ] [ atoms ] SI1 SI 0.000 1 C1 opls_069 0.000 1 C2 opls_069 0.000 1 C3 opls_069 0.000 1 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 C3 PDB file: ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00 ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00 ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00 ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00 ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00 ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00 ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00 ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00 ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00 ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00 ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00 ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00 ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00 TER Thanks a lot! On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > Your system works for me under Gromacs 4.0.4 - the only issue is that your > PDME residue has a net +0.3 charge. Does your Gromacs installation work > properly for proven systems like proteins? > > I would suggest upgrading to version 4.0.4 and trying again. If that does > not work, post to the list a complete description of your hardware and > software - OS, version, compilers used, configuration options, etc, and see > if anyone can spot a problem. > > -Justin > > Yanmei Song wrote: >> >> Sorry to bother so many times. >> >> I edited the rtp and added the new residue as following, which I think >> should be no problem. >> >> [ PDM ] >> >> [ atoms ] >> SI1 SI 0.300 1 >> C1 opls_069 0.000 1 >> C2 opls_069 0.000 1 >> O1 opls_108 -0.300 1 >> >> [ bonds ] >> SI1 -O1 >> SI1 C1 >> SI1 C2 >> SI1 O1 >> O1 +SI1 >> >> >> ; Terminal PDMS residue ("beginning" of chain) >> >> [ PDMB ] >> [ atoms ] >> C1 opls_069 0.000 1 >> SI1 SI 0.300 1 >> C2 opls_069 0.000 1 >> C3 opls_069 0.000 1 >> O1 opls_108 -0.300 1 >> >> [ bonds ] >> SI1 C1 >> SI1 C2 >> SI1 C3 >> SI1 O1 >> O1 +SI1 >> >> >> ; Terminal PDMS residue ("end" of chain) >> >> >> [ PDME ] >> [ atoms ] >> SI1 SI 0.300 1 >> C1 opls_069 0.000 1 >> C2 opls_069 0.000 1 >> C3 opls_069 0.000 1 >> >> [ bonds ] >> SI1 -O1 >> SI1 C1 >> SI1 C2 >> SI1 C3 >> >> Also my pdb is : >> >> ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00 >> ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00 >> ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00 >> ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00 >> ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00 >> ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00 >> ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00 >> ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00 >> ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00 >> ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00 >> ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00 >> ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00 >> ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00 >> TER >> >> after pdb2gmx, I still got the error: >> >> Opening library file ffoplsaa.rtp >> Opening library file >> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat >> Reading pdms2.pdb... >> Read 13 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 3 residues with 13 atoms >> >> chain #res #atoms >> 1 ' ' 3 13 >> >> 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: >> >> >> ------------------------------------------------------- >> >> Anyone knows where I did wrong? >> >> Thank you so much! >> 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 >>> >> >> >> > > -- > ======================================== > > 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