On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 6/10/13 8:42 AM, Justin Lemkul wrote: > >> >> >> On 6/10/13 8:40 AM, Steven Neumann wrote: >> >>> On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 6/10/13 8:23 AM, Steven Neumann wrote: >>>> >>>> Dear Gmx Users, >>>>> >>>>> I created my own CG force field and i process my structure to pdb2gmx. >>>>> I >>>>> process 3 beads I created to check whether the topology is properly >>>>> created: >>>>> >>>>> >>>>> Using the CG force field in directory ./CG.ff >>>>> >>>>> No file 'watermodels.dat' found, will not include a water model >>>>> Reading 60central_Carbons.pdb... >>>>> Read 3 atoms >>>>> Analyzing pdb file >>>>> Splitting chemical chains based on TER records or chain id changing. >>>>> There are 1 chains and 0 blocks of water and 3 residues with 3 atoms >>>>> >>>>> chain #res #atoms >>>>> 1 'X' 3 3 >>>>> >>>>> All occupancy fields zero. This is probably not an X-Ray structure >>>>> Opening force field file ./CG.ff/atomtypes.atp >>>>> Atomtype 1 >>>>> Reading residue database... (CG) >>>>> Opening force field file ./CG.ff/aminoacids.rtp >>>>> Reading .rtp file without '[ bondedtypes ]' directive, >>>>> Will proceed as if the entry >>>>> >>>>> >>>>> [ bondedtypes ] >>>>> ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 >>>>> remove_dih >>>>> 1 1 1 2 0 3 >>>>> 1 >>>>> 1 >>>>> Residue 13t at the beginning of ./CG.ff/aminoacids.rtp >>>>> Sorting it all out... >>>>> >>>>> Back Off! I just backed up topol.top to ./#topol.top.2# >>>>> Processing chain 1 'X' (3 atoms, 3 residues) >>>>> Identified residue MET1 as a starting terminus. >>>>> Identified residue VAL3 as a ending terminus. >>>>> 8 out of 8 lines of specbond.dat converted successfully >>>>> Checking for duplicate atoms.... >>>>> Now there are 3 residues with 3 atoms >>>>> Making bonds... >>>>> No bonds >>>>> Generating angles, dihedrals and pairs... >>>>> Making cmap torsions...There are 0 dihedrals, 0 impropers, 0 >>>>> angles >>>>> 0 pairs, 0 bonds and 0 virtual sites >>>>> Total mass 319.420 a.m.u. >>>>> Total charge 1.000 e >>>>> Writing topology >>>>> >>>>> Back Off! I just backed up posre.itp to ./#posre.itp.2# >>>>> >>>>> Writing coordinate file... >>>>> >>>>> Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# >>>>> --------- PLEASE NOTE ------------ >>>>> You have successfully generated a topology from:3Carbons.pdb. >>>>> The CG force field is used. >>>>> --------- ETON ESAELP ------------ >>>>> >>>>> gcq#304: "Gabba Gabba Hey!" (The Ramones) >>>>> >>>>> It stated that there are no angles. >>>>> However in my ffbonded.itp which i ncluded in my forcefield.itp >>>>> >>>>> [ angletypes ] >>>>> ; i j k funct th0 C0 C1 C2 C3 C4 >>>>> CME CSE CVA 6 0 0.0680894 -0.0328291000 590330 >>>>> -46.3 13 >>>>> >>>>> How Gromacs can read this angle? >>>>> >>>>> >>>>> [angletypes] simply define possible interactions, but are not used >>>> unless >>>> there are [angles] in the .rtp that use them. pdb2gmx writes angles >>>> based >>>> on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot >>>> write any angles. Does your .rtp entry specify [angles] but no [bonds]? >>>> >>> >>> >>> I want to use constraints with SHAKE as bonds...no harmonic bonds. In >>> this >>> case pdb2gmx will never create angles? Shall I also manually add [ >>> angles ] >>> to my top then? >>> >>> >> Yes, because in the absence of bonds, even [angles] in .rtp entries are >> ignored. >> >> > Thinking a bit more though, it's probably a lot easier to define bonds and > let pdb2gmx do the work for you. Using: > > constraints = all-bonds > constraint-algorithm = shake > > will turn all bonds in the topology into constraints, which sounds like > exactly what you want to do. > > > -Justin > I want my atoms to be constrained. I specified in my topology [ constraints ] 1 2 0.4 2 3 0.4 etc. Shall use? constraints = none constraint-algorithm = shake I do not have [ bonds ] in my topology > -- > ==============================**========== > > 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> > -- 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
