[gmx-users] doubt - how to fix all atoms ?
Luis Paulo
luis.scott at ufabc.edu.br
Mon Jul 27 18:00:21 CEST 2009
Please
I need to fix all atoms of a proetin and I need to calculte the initital
enregy without to exceute septs of dynsmics.
How can i do this ?
Thanks
best regrads
luis Scott
2009/7/27 <gmx-users-request at gromacs.org>
> Send gmx-users mailing list submissions to
> gmx-users at 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-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at 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. GHrace install (Samik Bhattacharya)
> 2. Re: GHrace install (Jussi Lehtola)
> 3. Re: About exclusion of non-bonded interaction for pairs of
> energy groups (Lee Soin)
> 4. RE: GHrace install (jimkress_58)
> 5. POSITION-RESTRAIN (Morteza Khabiri)
> 6. Re: POSITION-RESTRAIN (Mark Abraham)
> 7. Re: GHrace install (Mark Abraham)
> 8. Re: About exclusion of non-bonded interaction for pairs of
> energy groups (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 27 Jul 2009 16:48:57 +0530 (IST)
> From: Samik Bhattacharya <samikbhat at yahoo.co.in>
> Subject: [gmx-users] GHrace install
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID: <224940.85000.qm at web95411.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hi alli'm facing alot of trouble in installing grace in my redhat machine.
> its always complaining about Motiff API. ive installed Lesstiff but even
> afetr that grace is not getting installed...i can't make out how to install
> it? is there any problem in the path? should i've to set path before grace
> install. i've gone through several pages about grace installation but with
> no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat?
> thanking you all
> Shamik
>
>
>
> See the Web's breaking stories, chosen by people like you. Check
> out Yahoo! Buzz. http://in.buzz.yahoo.com/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a13124cb/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Mon, 27 Jul 2009 14:28:31 +0300
> From: Jussi Lehtola <jussi.lehtola at helsinki.fi>
> Subject: Re: [gmx-users] GHrace install
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1248694111.5152.2.camel at hawking.theorphys.helsinki.fi>
> Content-Type: text/plain
>
> On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote:
> > hi alli'm facing alot of trouble in installing grace in my redhat
> > machine. its always complaining about Motiff API.. ive installed
> > Lesstiff but even afetr that grace is not getting installed....i can't
> > make out how to install it? is there any problem in the path? should
> > i've to set path before grace install. i've gone through several pages
> > about grace installation but with no effect.ac anyone pls tell me how
> > to install Grace in Fedora of Redhat?
>
> You should avoid compiling software yourself, because that beats the
> whole idea of having a) a distribution that has ready-to-use software
> and b) a package management system that makes upgrades possible.
>
> In Fedora
> # yum -y install grace
>
> In RHEL, first enable the Fedora EPEL repository with
> # rpm -Uvh \
>
> http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm
> and then install grace with
> # yum -y install grace
>
> Then you can run grace with $ xmgrace
> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50632
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 27 Jul 2009 21:56:08 +0800
> From: Lee Soin <nomadoro at gmail.com>
> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for
> pairs of energy groups
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <e2838e4e0907270656n4be59b34w4488a610fefd4299 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I see in the .top file generated by pdb2gmx:
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
>
> The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
> c2 and c3 parametrize electrostatic interactions? And what do they stand
> for
> respectively? Thanks!
>
>
> 2009/7/27 Mark Abraham <Mark.Abraham at anu.edu.au>
>
> > Lee Soin wrote:
> >
> >> My problem is actually as follows:
> >>
> >
> > Please describe in as full detail as reasonable the first time :-)
> >
> > I have three groups of atoms: A, B and C. Now I want to keep full
> >> interaction between A-B and A-C, but only retain the repulsive part of
> VDW
> >> interaction between B-C. I'm using the OPLS force field. It seems to me
> >> that
> >> the parameters for OPLS in the .itp files are specified for each atom,
> so
> >> is
> >> there any way to treat the interaction pairwise?
> >>
> >
> > Yes, use [ pairs ] directives to overrride the atomtype-based lookup.
> That
> > will be tedious if there are many such atoms. Read parts of chapter 5.
> >
> > Probably, no force field was parameterized to reproduce whatever it is
> > you're trying to observe.
> >
> >
> > Mark
> > _______________________________________________
> > 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
> >
>
>
>
> --
> SUN Li
> Department of Physics
> Nanjing University, China
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a579dfe1/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Mon, 27 Jul 2009 10:44:33 -0400
> From: "jimkress_58" <jimkress_58 at kressworks.org>
> Subject: RE: [gmx-users] GHrace install
> To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
> Message-ID: <D3E11AB6F6DC42AA8891734A1EF5BE9E at libraryPC>
> Content-Type: text/plain; charset="us-ascii"
>
> If you are using a vanilla RedHat system, the yum method will work.
> However, if you are using a prepackaged clustering environment (like ROCKS)
> you may break it.
>
> All you nee to know to install grace is the location of the headers and
> libraries for Lesstiff. You then supply them to grace as a part of the
> ./configure command and things should go smoothly.
>
> It's unfortunate the person who wrote and maintains grace is unwilling to
> provide this information to the people that want to use grace. However,
> you
> can't stop people from being jerks. That's why I'd prefer gromacs use a
> different plotting package like gnuplot.
>
> Jim
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Samik Bhattacharya
> Sent: Monday, July 27, 2009 7:19 AM
> To: Gromacs
> Subject: [gmx-users] GHrace install
>
> hi alli'm facing alot of trouble in installing grace in my redhat machine.
> its always complaining about Motiff API.. ive installed Lesstiff but even
> afetr that grace is not getting installed....i can't make out how to
> install
> it? is there any problem in the path? should i've to set path before grace
> install. i've gone through several pages about grace installation but with
> no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat?
> thanking you all
> Shamik
>
>
> ________________________________
>
> Looking for local information? Find it on Yahoo! Local
> <http://in.rd.yahoo.com/tagline_local_1/*http://in.local.yahoo.com/>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 27 Jul 2009 16:05:37 +0200 (CEST)
> From: "Morteza Khabiri" <khabiri at greentech.cz>
> Subject: [gmx-users] POSITION-RESTRAIN
> To: gmx-users at gromacs.org
> Message-ID:
> <21935.160.217.215.149.1248703537.squirrel at www.greentech.cz>
> Content-Type: text/plain;charset=iso-8859-2
>
> Dear gmxusers.
>
> I want to restrain the lipids in my system which contains protein,lipid
> and water. I make the restraint itp file by genpr then I added it in
> toplogy file.
> After doing grompp to make tpr file I get the following message:
>
> Fatal error:
> [ file "posre_entirelipid1.itp", line 56 ]:
> Atom index (53) in position_restraints out of bounds (1-52)
> I found the similar error in the mailing list and they suggested probably
> the place of restraint itp file which was included in topology file is
> wrong. However, I tried several positions for restraint itp but I think
> it is not the
> solution. Do you have any other suggestion about this problem??????
>
> Thanks
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 28 Jul 2009 01:04:51 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] POSITION-RESTRAIN
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A6DC213.1000700 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-2; format=flowed
>
> Morteza Khabiri wrote:
> > Dear gmxusers.
> >
> > I want to restrain the lipids in my system which contains protein,lipid
> > and water. I make the restraint itp file by genpr then I added it in
> > toplogy file.
> > After doing grompp to make tpr file I get the following message:
> >
> > Fatal error:
> > [ file "posre_entirelipid1.itp", line 56 ]:
> > Atom index (53) in position_restraints out of bounds (1-52)
> > I found the similar error in the mailing list and they suggested probably
> > the place of restraint itp file which was included in topology file is
> > wrong. However, I tried several positions for restraint itp but I think
> > it is not the
> > solution. Do you have any other suggestion about this problem??????
>
> You're using a [ position_restraints ] directive that requires at least
> 53 atoms in a position where only 52 are defined. There are various
> explanations, including #including in the wrong place, or #including a
> wrong file. Look carefully at a correct example.
>
> Mark
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 28 Jul 2009 01:06:30 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] GHrace install
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A6DC276.8050001 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> jimkress_58 wrote:
> > If you are using a vanilla RedHat system, the yum method will work.
> > However, if you are using a prepackaged clustering environment (like
> ROCKS)
> > you may break it.
> >
> > All you nee to know to install grace is the location of the headers and
> > libraries for Lesstiff. You then supply them to grace as a part of the
> > ./configure command and things should go smoothly.
> >
> > It's unfortunate the person who wrote and maintains grace is unwilling to
> > provide this information to the people that want to use grace. However,
> you
> > can't stop people from being jerks. That's why I'd prefer gromacs use a
> > different plotting package like gnuplot.
>
> Agreed, although it is straightforward to use gnuplot anyway. See
> http://oldwiki.gromacs.org/index.php/Graphing_Data
>
> Mark
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 28 Jul 2009 01:10:53 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for
> pairs of energy groups
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A6DC37D.6020407 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Lee Soin wrote:
> > I see in the .top file generated by pdb2gmx:
> > [ pairs ]
> > ; ai aj funct c0 c1 c2 c3
> >
> > The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3.
> Do
> > c2 and c3 parametrize electrostatic interactions? And what do they stand
> for
> > respectively? Thanks!
>
> No, they're two pairs of VDW parameters, one pair each for two possible
> states for a free-energy calculation. The tables in chapter 5 imply
> this, but it is not at all obvious to a newcomer.
>
> >> Yes, use [ pairs ] directives to overrride the atomtype-based lookup.
> That
> >> will be tedious if there are many such atoms. Read parts of chapter 5.
>
> You should still do this.
>
> Mark
>
>
> ------------------------------
>
> _______________________________________________
> 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 63, Issue 131
> ******************************************
>
--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de Matemática, Computação e Cognição
Universidade Federal do ABC
Grupo de Pesquisa em Biologia Computacional
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090727/0e47ea8e/attachment.html>
More information about the gromacs.org_gmx-users
mailing list