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? > > > In terms of bonds I want to use constraints, can I use in my ffbonded.itp >> [ >> costrainttypes] or add them automatically after? >> >> > You would need [constraints] in your .top file, not [constrainttypes] > (same hierarchy as described above with angles). Usually .mdp keywords > serve better than topology modifications in the case of constraints, unless > you're only constraining a subset of atoms within a single [moleculetype]. > I can manually add [ constraints ] to my top after processing with pdb2gmx > > -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? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
