Thank you Justin. I have now the topology. I have a quick question regarding atom types. I used opls_143 and opls_144 for C and H of ethylene respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe these are not the proper atomtypes for H2C=CH2.
rtp entry: [ atoms ] C1 opls_143 -0.120 1 H11 opls_144 0.060 1 H12 opls_144 0.060 1 C2 opls_143 -0.120 2 H21 opls_144 0.060 2 H22 opls_144 0.060 2 >From atomtypes.atp opls_141 12.01100 ; alkene C (R2-C=) opls_142 12.01100 ; alkene C (RH-C=) * opls_143 12.01100 ; alkene C (H2-C=) opls_144 1.00800 ; alkene H (H-C=)* Did I select the correct atomtypes? Thanks many times! On 4 April 2013 18:23, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/4/13 6:17 PM, Juliette N. wrote: > >> Hi Justin, >> >> Thanks a lot for your message. I am petrified why pdb2gmx is not >> recognizing the residue ETY. This the first residue added to ffoplsaa.rtp >> but as you may see below it is not read from rtp. >> >> I am sure this residue is added to ffoplsaa.rtp which is existing in the >> working directory: >> >> [ ETY ] >> [ atoms ] >> C1 opls_143 -0.120 1 >> H11 opls_144 0.060 1 >> H12 opls_144 0.060 1 >> C2 opls_143 -0.120 2 >> H21 opls_144 0.060 2 >> H22 opls_144 0.060 2 >> >> [ bonds ] >> C1 H11 >> C1 H12 >> C1 C2 >> C2 H21 >> C2 H22 >> ;C2 C1 >> >> Then I issue: >> >> pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa >> :-) G R O M A C S (-: >> >> GROwing Monsters And Cloning Shrimps >> >> :-) VERSION 4.5.4 (-: >> >> Using the Oplsaa force field in directory oplsaa.ff >> >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**watermodels.dat >> >> Select the Water Model: >> 1: TIP4P TIP 4-point, recommended >> 2: TIP3P TIP 3-point >> 3: TIP5P TIP 5-point >> 4: SPC simple point charge >> 5: SPC/E extended simple point charge >> 6: None >> 6 >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.r2b >> Reading Ethylene.gro... >> Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms >> Analyzing pdb file >> Splitting PDB chains based on TER records or changing chain id. >> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms >> >> chain #res #atoms >> 1 ' ' 1 6 >> >> No occupancies in Ethylene.gro >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomtypes.atp >> Atomtype 1 >> Reading residue database... (oplsaa) >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.rtp >> Residue 56 >> Sorting it all out... >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.hdb >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.n.tdb >> Opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.c.tdb >> >> Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1# >> Processing chain 1 (6 atoms, 1 residues) >> There are 0 donors and 0 acceptors >> There are 0 hydrogen bonds >> Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. >> Problem with chain definition, or missing terminal residues. >> This chain does not appear to contain a recognized chain molecule. >> If this is incorrect, you can edit residuetypes.dat to modify the >> behavior. >> 8 out of 8 lines of specbond.dat converted successfully >> >> ------------------------------**------------------------- >> Program pdb2gmx, VERSION 4.5.4 >> Source code file: resall.c, line: 581 >> >> Fatal error: >> Residue 'ETY' not found in residue topology database >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> >> >> I am kind of baffled what could be wrong. I would really appreciate if you >> could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I >> doubt)? >> Do i have to edit esiduetypes.dat? >> >> > You've added the .rtp entry incorrectly. pdb2gmx in version 4.5 and above > needs .rtp files to be organized in force field subdirectories (in your > case oplsaa.ff). It will not recognize a file called "ffoplsaa.rtp," which > is the pre-4.5 syntax for force field files. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
