Hi, everyone I've just tried x2top.
My ffoplsaa.n2t file is as follows ;atom atom_type charge mass neighbor_N neighbor distance O opls_002 -0.3 15.9994 2 SI 0.160 SI 0.160 O opls_002 -0.3 15.9994 1 SI 0.160 SI SI 0.6 28.08 1 O 0.160 SI SI 0.6 28.08 2 O 0.160 O 0.160 SI SI 0.6 28.08 3 O 0.160 O 0.160 O 0.160 SI SI 0.6 28.08 4 O 0.160 O 0.160 O 0.160 O 0.160 I entered the command below: x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa here's my output: chen...@chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa :-) G R O M A C S (-: Giant Rising Ordinary Mutants for A Clerical Setup :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) x2top (-: Option Filename Type Description ------------------------------------------------------------ -f SiO2.pdb Input Structure file: gro g96 pdb tpr tpb tpa -o SiO2.top Output, Opt! Topology file -r out.rtp Output, Opt. Residue Type file used by pdb2gmx Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -ff string oplsaa Force field for your simulation. Type "select" for interactive selcection. -[no]v bool no Generate verbose output in the top file. -nexcl int 3 Number of exclusions -[no]H14 bool yes Use 3rd neighbour interactions for hydrogen atoms -[no]alldih bool no Generate all proper dihedrals -[no]remdih bool no Remove dihedrals on the same bond as an improper -[no]pairs bool yes Output 1-4 interactions (pairs) in topology file -name string SIO2 Name of your molecule -[no]pbc bool yes Use periodic boundary conditions. -[no]pdbq bool no Use the B-factor supplied in a pdb file for the atomic charges -[no]param bool yes Print parameters in the output -[no]round bool yes Round off measured values -kb real 400000 Bonded force constant (kJ/mol/nm^2) -kt real 400 Angle force constant (kJ/mol/rad^2) -kp real 5 Dihedral angle force constant (kJ/mol/rad^2) Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file ffoplsaa.n2t Opening library file ffoplsaa.n2t There are 6 name to type translations Generating bonds from distances... atom 0 (Here it stopped but not existed)\ Di Cheng University of Science and Technology of China Hefei, Anhui Province 230026 P. R. China E-mail: chen...@mail.ustc.edu.cn Tel.: +86-15321055911 On Tue, Mar 23, 2010 at 7:00 PM, <gmx-users-requ...@gromacs.org> wrote: > 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. Re: [help]How to produce .top file from Material Studio (Yang Ye) > 2. Re: [help]How to produce .top file from Material Studio > (szewc...@ualberta.ca) > 3. new/old gromacs-wiki (Christian Seifert) > 4. Dynamics cross correlation map (sukesh chandra gain) > 5. Re: Dynamics cross correlation map (Tsjerk Wassenaar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Mar 2010 10:37:36 +0800 > From: Yang Ye <leafyo...@yahoo.com> > Subject: Re: [gmx-users] [help]How to produce .top file from Material > Studio > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <1b3c3eeb1003221937r6846de78le49635f8fe76c...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > No way from MS. Check x2top. > > Yang YE > > On Mon, Mar 22, 2010 at 10:42 PM, 程迪 <chengdi123...@gmail.com> wrote: > > > Hi,everyone > > > > I have build a SiO2 structure in Material Studio, And I've set the xyz > > coordinates and force field parameters of the structure. Is there some > tool > > or method to produce a .top file from MS. I do not want to write .top > file > > line by line. > > > > Thanks. > > > > Di Cheng > > > > University of Science and Technology of China > > Hefei, Anhui Province 230026 > > P. R. China > > E-mail: chen...@mail.ustc.edu.cn > > Tel.: +86-15321055911 > > > > > > -- > > 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 > > > > > > -- > Regards, > Yang Ye > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100323/ee9ef0ce/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 22 Mar 2010 22:54:04 -0600 > From: szewc...@ualberta.ca > Subject: Re: [gmx-users] [help]How to produce .top file from Material > Studio > To: gmx-users@gromacs.org > Message-ID: <20100322225404.14850saq7v861...@webmail.ualberta.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > I run my simulations in Gromacs but I generated my structure in > Materials Studio as well and I agree with Yang Ye - MS will not give > you the .top. > It`s either x2top or by hand if your system is quite simple or if you > can create a topology of one molecule which then can be multiplied > with genconf and/or editconf in Gromacs. > > Good luck! > > Paula > > > Quoting "Yang Ye" <leafyo...@yahoo.com>: > > > No way from MS. Check x2top. > > > > Yang YE > > > > On Mon, Mar 22, 2010 at 10:42 PM, ?? <chengdi123...@gmail.com> wrote: > > > >> Hi,everyone > >> > >> I have build a SiO2 structure in Material Studio, And I've set the xyz > >> coordinates and force field parameters of the structure. Is there some > tool > >> or method to produce a .top file from MS. I do not want to write .top > file > >> line by line. > >> > >> Thanks. > >> > >> Di Cheng > >> > >> University of Science and Technology of China > >> Hefei, Anhui Province 230026 > >> P. R. China > >> E-mail: chen...@mail.ustc.edu.cn > >> Tel.: +86-15321055911 > >> > >> > >> -- > >> 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 > >> > > > > > > > > -- > > Regards, > > Yang Ye > > > > > > ------------------------------ > > Message: 3 > Date: 23 Mar 2010 11:38:42 +0100 > From: "Christian Seifert" <cseif...@bph.ruhr-uni-bochum.de> > Subject: [gmx-users] new/old gromacs-wiki > To: gmx-users@gromacs.org > Message-ID: <1269340722.4755.5.ca...@moganshan> > Content-Type: text/plain > > Hi. > > I can not use the oldwiki.gromacs.org . The page seems to be down. And > wiki.gromacs.org is a room booking system for the biophysics department > of the University of Stockholm (showing that the CBR kitchen is booked > for Computational protein science today^^). > > Greets, > Christian > > -- > M.Sc. Christian Seifert > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: cseif...@bph.rub.de > Web: http://www.bph.rub.de > > > > ------------------------------ > > Message: 4 > Date: Tue, 23 Mar 2010 16:14:48 +0530 > From: sukesh chandra gain <suk...@atc.tcs.com> > Subject: [gmx-users] Dynamics cross correlation map > To: gmx-users@gromacs.org > Message-ID: <4ba89ba0.4070...@atc.tcs.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear All, > > Could you please tell how to get the Dynamic Cross Correlation map > with Gromacs analysis tool or other tools. I want to know over a 20 ns > simulation whether the motions of two residues or group of residues are > correlated or anti correlated. For this I want to plot a dynamics cross > correlation map in which I could get the precise information of group of > atoms. > I have done the following step and got the covariance matrix but don't > know how to proceed further. > >g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l > covar.log -xpm covar.xpm -ascii covar.dat > Waiting for your input. > > Thank You, > Regards, > Sukesh > > -- > Sukesh Chandra Gain > TCS Innovation Labs > Tata Consultancy Services Ltd. > 'Deccan Park', Madhapur > Hyderabad 500081 > Phone: +91 40 6667 3572 > > > > ------------------------------ > > Message: 5 > Date: Tue, 23 Mar 2010 11:54:52 +0100 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] Dynamics cross correlation map > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <8ff898151003230354q15b3591bw2e531a1edbb8b...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Sukesh, > > You've posted this question several times now, without changing the > phrasing. Did it occur to you that maybe nobody felt equipped to or > sufficiently triggered by your post to reply? What do you mean with a > 'dynamics cross correlation map' for 'residues or groups of residues'? > Being more explicit, also pointing to some references or giving some > formulas, might help you get a response. > But isn't your answer already in the image covar.xpm? Otherwise, maybe > using the atomic covariances (-xpma) might do what you want. If not, > your problem is not as trivial as you may think. > > Cheers, > > Tsjerk > > On Tue, Mar 23, 2010 at 11:44 AM, sukesh chandra gain > <suk...@atc.tcs.com> wrote: > > Dear All, > > > > Could you please tell how to get the Dynamic Cross Correlation map with > > Gromacs analysis tool or other tools. I want to know over a 20 ns > simulation > > whether the motions of two residues or group of residues are correlated > or > > anti correlated. For this I want to plot a dynamics cross correlation map > in > > which I could get the precise information of group of atoms. > > I have done the following step and got the covariance matrix but don't > know > > how to proceed further. > >>g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l > >> covar.log -xpm covar.xpm -ascii covar.dat > > Waiting for your input. > > > > Thank You, > > Regards, > > Sukesh > > > > -- > > Sukesh Chandra Gain > > TCS Innovation Labs > > Tata Consultancy Services Ltd. > > 'Deccan Park', Madhapur > > Hyderabad 500081 > > Phone: +91 40 6667 3572 > > > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > > ------------------------------ > > -- > 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 71, Issue 105 > ****************************************** >
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