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-requ...@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. 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 <samikb...@yahoo.co.in> > Subject: [gmx-users] GHrace install > To: Gromacs <gmx-users@gromacs.org> > Message-ID: <224940.85000...@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.leht...@helsinki.fi> > Subject: Re: [gmx-users] GHrace install > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <1248694111.5152.2.ca...@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.leht...@helsinki.fi, p. 191 50632 > ------------------------------------------------------ > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > jussi.leht...@helsinki.fi > ------------------------------------------------------ > > > > ------------------------------ > > Message: 3 > Date: Mon, 27 Jul 2009 21:56:08 +0800 > From: Lee Soin <nomad...@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@gromacs.org> > Message-ID: > <e2838e4e0907270656n4be59b34w4488a610fefd4...@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.abra...@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@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 > > > > > > -- > 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...@kressworks.org> > Subject: RE: [gmx-users] GHrace install > To: "'Discussion list for GROMACS users'" <gmx-users@gromacs.org> > Message-ID: <d3e11ab6f6dc42aa8891734a1ef5b...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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" <khab...@greentech.cz> > Subject: [gmx-users] POSITION-RESTRAIN > To: gmx-users@gromacs.org > Message-ID: > <21935.160.217.215.149.1248703537.squir...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] POSITION-RESTRAIN > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a6dc213.1000...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] GHrace install > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a6dc276.8050...@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.abra...@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@gromacs.org> > Message-ID: <4a6dc37d.6020...@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@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
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