Hello Justin, thank you for answering! I think I already have done what you suggested when I created my ffbonded.itp and .rtp files.
I am sending a piece of my topology and ffbonded.itp files. Follows also the residue from .rtp and the configuration of glycol (.gro) so you can consider where I might be wrong and what I still must do. Thanks again. eef !!! topol.top !!! ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 HCP1 1 PA2 HOA 1 0.42 1.008 ; qtot 0.42 2 OC311 1 PA2 OHA 1 -0.65 15.9994 ; qtot -0.23 3 CC322 1 PA2 CA 1 0.05 12.011 ; qtot -0.18 4 HCA2 1 PA2 HA1 1 0.09 1.008 ; qtot -0.09 ... [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 2 3 1 3 4 1 ... [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 1 5 1 1 6 1 ... [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 5 2 3 4 5 ... [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 9 ... !!! ffbonded.itp !!! [ bondtypes ] ; i j func b0 kb OC311 HCP1 1 0.0960 456056.0 ; par22 OH1 H CC322 OC311 1 0.1420 334720.0 ; adm 11/08, glycerol CC322 HCA2 1 0.1111 258571.2 ; par22 HA CT2 [ angletypes ] ; i j k func th0 cth ub0 cub HCP1 OC311 CC312 5 106.00 412.40 0.0 0.00 ; og 1/06 EtOH IR fit [ dihedraltypes ] ; i j k l func phi0 cp mult HCP1 OC311 CC322 HCA2 9 0.0 0.75 3 ; og methanol !!! file.rtp !!! [ PA2 ] ; Glycol [ atoms ] HOA HCP1 0.420 1 OHA OC311 -0.650 1 CA CC322 0.050 1 HA1 HCA2 0.090 1 HA2 HCA2 0.090 1 CB CC322 0.050 2 HB1 HCA2 0.090 2 HB2 HCA2 0.090 2 OHB OC311 -0.650 2 HOB HCP1 0.420 2 [ bonds ] OHA HOA OHA CA CA HA1 CA HA2 CB CA CB HB1 CB HB2 OHB CB HOB OHB !!! conf.gro !!! GROningen MAchine for Chemical Simulation 10 1PA2 HOA 1 -0.248 -0.048 0.000 1PA2 OHA 2 -0.177 0.017 0.000 1PA2 CA 3 -0.052 -0.052 0.000 1PA2 HA1 4 -0.041 -0.115 0.089 1PA2 HA2 5 -0.041 -0.115 -0.089 1PA2 CB 6 0.057 0.054 0.000 1PA2 HB1 7 0.046 0.117 -0.089 1PA2 HB2 8 0.046 0.117 0.089 1PA2 OHB 9 0.182 -0.015 0.000 1PA2 HOB 10 0.253 0.049 0.000 3.00000 3.00000 3.00000 _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br > ---------- Forwarded message ---------- > From: <gmx-users-requ...@gromacs.org> > Date: Mon, Aug 23, 2010 at 7:00 AM > Subject: gmx-users Digest, Vol 76, Issue 113 > To: gmx-users@gromacs.org > > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Metallic boundary conditions (poj...@icp.uni-stuttgart.de) > 2. Charmm to Gromacs: Polyols force field (Eudes Fileti) > 3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul) > 4. PMF (abdul wadood) > 5. Re: please, how edr data is xdr packed? (Sander Pronk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Aug 2010 17:52:46 +0200 > From: poj...@icp.uni-stuttgart.de > Subject: [gmx-users] Metallic boundary conditions > To: gmx-users@gromacs.org > Message-ID: > <3e5fe7757a687609503cad715e2a5d15.squir...@www.icp.uni-stuttgart.de > > > Content-Type: text/plain;charset=iso-8859-1 > > > Hi, > > thank you for your answer. What is then epsilon_r ? > > regards. > > > > ------------------------------ > > Message: 2 > Date: Sun, 22 Aug 2010 14:42:43 -0300 > From: Eudes Fileti <fil...@ufabc.edu.br> > Subject: [gmx-users] Charmm to Gromacs: Polyols force field > To: gmx-users@gromacs.org > Message-ID: > > <aanlktikqtlshdgqsmprykc0x0fjiq+c_ydzcm6pke...@mail.gmail.com<aanlktikqtlshdgqsmprykc0x0fjiq%2bc_ydzcm6pke...@mail.gmail.com> > > > Content-Type: text/plain; charset="windows-1252" > > Olá pessoal, > > Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009, > 5, 1315). > I am very interested in using it in GROMACS. > > For this, I began the transfer of the parameters with the following recipe: > > 1) All atom types were added to the atomtypes.atp file; > 2) All bonded parameters (bonds, angles, ub, dihedral and impropers) > were added to the ffbonded.itp file; > 3) van der Waals and Coulomb parameters were inserted properly > in ffnonbonded.itp; > 4) The residues were created in a new file named polyols.rtp. > > Well, pdb2gmx works fine! It generates the restraints file (posre.itp), > configuration file > (conf.gro) and topology file (topol.itp). But when I run it in grommp, the > default for > parameters are not found. Something like: > > ERROR 6 [file topol.top, line 40]: > No default Bond types > > I know I can insert the parameters by hand in each .top file generated by > pdb2gmx. > But what I need to do, so that grompp recognizes the default values > automatically. > > Did I forgot some file? I'm making some mistake? > > Any suggestion is welcome! > > Muito obrigado! > eef > > _______________________________________ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC — CCNH > Av. dos Estados, 5001 > Santo André - SP - Brasil > CEP 09210-971 > +55.11.4996-0196 > http://fileti.ufabc.edu.br > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100822/8581cfd9/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Sun, 22 Aug 2010 13:46:39 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c71627f.1000...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > Eudes Fileti wrote: > > Olá pessoal, > > > > Recently, McKerrel published his CHARMM force field to polyols (JCTC, > > 2009, 5, 1315). > > I am very interested in using it in GROMACS. > > > > For this, I began the transfer of the parameters with the following > recipe: > > > > 1) All atom types were added to the atomtypes.atp file; > > 2) All bonded parameters (bonds, angles, ub, dihedral and impropers) > > were added to the ffbonded.itp file; > > 3) van der Waals and Coulomb parameters were inserted properly > > in ffnonbonded.itp; > > 4) The residues were created in a new file named polyols.rtp. > > > > Well, pdb2gmx works fine! It generates the restraints file (posre.itp), > > configuration file > > (conf.gro) and topology file (topol.itp). But when I run it in grommp, > > the default for > > parameters are not found. Something like: > > > > ERROR 6 [file topol.top, line 40]: > > No default Bond types > > > > I know I can insert the parameters by hand in each .top file generated > > by pdb2gmx. > > But what I need to do, so that grompp recognizes the default values > > automatically. > > > > Did I forgot some file? I'm making some mistake? > > > > Look on line 40 of the topology and see which atoms grompp is complaining > about. > You likely forgot to define the parameters for that particular bond type. > > -Justin > > > Any suggestion is welcome! > > > > Muito obrigado! > > eef > > > > _______________________________________ > > Eudes Eterno Fileti > > Centro de Ciências Naturais e Humanas > > Universidade Federal do ABC — CCNH > > Av. dos Estados, 5001 > > Santo André - SP - Brasil > > CEP 09210-971 > > +55.11.4996-0196 > > http://fileti.ufabc.edu.br > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Mon, 23 Aug 2010 06:23:39 +0000 > From: abdul wadood <wadoodbiochem...@hotmail.com> > Subject: [gmx-users] PMF > To: gromacs <gmx-users@gromacs.org> > Message-ID: <bay121-w7c84bc40d94bebf163356d0...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, All > > I am trying to calculate pmf for enzyme ligand complex using the tutorial > of umbrella sampling. > I have successfully created the unit cell around the protein and have > solvated. The ions were also added by genion. > But when I run the minimization step with the command > grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr > the following error comes > > > Fatal error: > Molecule type 'NA+' contains no atoms > > > I tried my best to solve the problem but could no succeeded. > Any help to solve this problem will be highly appreciated. > The topology file is attached. > > Thanks in advace > > Many regards > > Abdul Wadood, > Research Scholar, > Dr.Panjwani Center for Molecular Medicine and > Drug Research, > International Center for Chemical and > Biological Science, > University of Karachi, Karachi-75720, Pakistan. > Email:wadoodbiochem...@hotmail.com <email%3awadoodbiochem...@hotmail.com> > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/6c9f9ed2/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 23 Aug 2010 09:56:26 +0200 > From: Sander Pronk <pr...@cbr.su.se> > Subject: Re: [gmx-users] please, how edr data is xdr packed? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se> > Content-Type: text/plain; charset="us-ascii" > > As David said, the reading/writing is done in src/gmxlib/enxio.c, but you > could also read edr files indirectly through gmxdump: that should also give > you an idea of the type of information in those files. > > > > On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote: > > > Hi there, > > > > I am trying to use python xdrlib module to read edr files but not knowing > how the data is packed using the xdr protocol makes my work very difficult, > if not impossible. > > > > Would someone kindly tell me how data is packed in the edr file? Or where > it is the gromacs code so I can try to figure out a way? > > > > I've read http://tools.ietf.org/html/rfc1832.html and for reference, see > topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION". > > > > My other option would be using a parsing code to read g_energy output but > this seems very silly. > > > > Many thanks in advance, > > > > Alan > > > > -- > > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > > Department of Biochemistry, University of Cambridge. > > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > > >>http://www.bio.cam.ac.uk/~awd28<< > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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? Read http://www.gromacs.org/mailing_lists/users.php > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/4a7ed781/attachment-0001.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 76, Issue 113 > ****************************************** > >
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