On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 6/10/13 8:53 AM, Steven Neumann wrote: > >> 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 >>> >>> >> Thank you. But specifying [ bonds ] in my rtp file without force constant? >> > > Entries need to be syntactically correct, but the force constant is > completely irrelevant if you are constraining all bonds. > > > Shall i remove [ bonds ] from my top file then? >> >> > What? Without [bonds], you can't do what I'm suggesting. If you don't > have [bonds], you have to write [constraints] and [angles] (and any other > bonded directories) manually. > I am saying about removing them from top after pdb2gmx just to bring [ angles ] to top - I do not want to have a harmonic or any potential for bonds. > > -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? 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