On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul <[email protected]> wrote:
> > > On 6/10/13 9:22 AM, Steven Neumann wrote: > >> 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 +/-? >> >> > Look in any .rtp file that comes with Gromacs. In your case, it is even > easier than an atomistic force field. > > -Justin > Obviously... sorry for this question. Thank you. Steven > > >> >>> >>> 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<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<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> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<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? 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> >>>>> > >>>>> <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://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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