On Sat, Apr 6, 2013 at 5:56 AM, Juliette N. <joojoojo...@gmail.com> wrote:
> 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. > http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds Mark > > 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 > -- 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