[gmx-users] Re: gmx-users Digest, Vol 71, Issue 105
程迪
chengdi123000 at gmail.com
Tue Mar 23 13:03:10 CET 2010
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:
chengdi at 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: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911
On Tue, Mar 23, 2010 at 7:00 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: [help]How to produce .top file from Material Studio (Yang Ye)
> 2. Re: [help]How to produce .top file from Material Studio
> (szewczyk at 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 <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] [help]How to produce .top file from Material
> Studio
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <1b3c3eeb1003221937r6846de78le49635f8fe76c2c4 at 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 <chengdi123000 at 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: chengdi at mail.ustc.edu.cn
> > Tel.: +86-15321055911
> >
> >
> > --
> > gmx-users mailing list gmx-users at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Regards,
> Yang Ye
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> ------------------------------
>
> Message: 2
> Date: Mon, 22 Mar 2010 22:54:04 -0600
> From: szewczyk at ualberta.ca
> Subject: Re: [gmx-users] [help]How to produce .top file from Material
> Studio
> To: gmx-users at gromacs.org
> Message-ID: <20100322225404.14850saq7v861ieo at 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" <leafyoung at yahoo.com>:
>
> > No way from MS. Check x2top.
> >
> > Yang YE
> >
> > On Mon, Mar 22, 2010 at 10:42 PM, ?? <chengdi123000 at 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: chengdi at mail.ustc.edu.cn
> >> Tel.: +86-15321055911
> >>
> >>
> >> --
> >> gmx-users mailing list gmx-users at 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-request at 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" <cseifert at bph.ruhr-uni-bochum.de>
> Subject: [gmx-users] new/old gromacs-wiki
> To: gmx-users at gromacs.org
> Message-ID: <1269340722.4755.5.camel at 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: cseifert at bph.rub.de
> Web: http://www.bph.rub.de
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Mar 2010 16:14:48 +0530
> From: sukesh chandra gain <sukesh at atc.tcs.com>
> Subject: [gmx-users] Dynamics cross correlation map
> To: gmx-users at gromacs.org
> Message-ID: <4BA89BA0.4070707 at 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 <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Dynamics cross correlation map
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <8ff898151003230354q15b3591bw2e531a1edbb8b26a at 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
> <sukesh at 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 at 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-request at 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 at 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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