On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul <[email protected]> wrote:
> > > On 6/10/13 9:11 AM, Steven Neumann wrote: > >> 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? >> >> > Each .rtp entry should only contain one bead, right? The only way to > define angles for such a system is to use +/- prefixes for succeeding and > preceding residues (beads). > > -Justin > Yes, indeed. Can you provide me the example of such +/-? > > >> 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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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