Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids?
On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/10/13 9:04 AM, Steven Neumann wrote: > >> On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 6/10/13 8:53 AM, Steven Neumann wrote: >>> >>> On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul <[email protected]> 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 <[email protected]> >>>>>> >>>>>>> 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. >> >> > I suppose you can do that, but why bother? If you want to constrain all > bonds with SHAKE, see above. There will be no harmonic potential anywhere > if all bonds are constrained. > > > -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 [email protected] > 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 [email protected]. > * Can't post? 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