<div>Please</div>
<div> </div>
<div> I need to fix all atoms of a proetin and I need to calculte the initital enregy without to exceute septs of dynsmics. </div>
<div>How can i do this ?</div>
<div> </div>
<div>Thanks</div>
<div>best regrads</div>
<div>luis Scott<br><br></div>
<div class="gmail_quote">2009/7/27 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. GHrace install (Samik Bhattacharya)<br> 2. Re: GHrace install (Jussi Lehtola)<br>
3. Re: About exclusion of non-bonded interaction for pairs of<br> energy groups (Lee Soin)<br> 4. RE: GHrace install (jimkress_58)<br> 5. POSITION-RESTRAIN (Morteza Khabiri)<br> 6. Re: POSITION-RESTRAIN (Mark Abraham)<br>
7. Re: GHrace install (Mark Abraham)<br> 8. Re: About exclusion of non-bonded interaction for pairs of<br> energy groups (Mark Abraham)<br><br><br>----------------------------------------------------------------------<br>
<br>Message: 1<br>Date: Mon, 27 Jul 2009 16:48:57 +0530 (IST)<br>From: Samik Bhattacharya <<a href="mailto:samikbhat@yahoo.co.in">samikbhat@yahoo.co.in</a>><br>Subject: [gmx-users] GHrace install<br>To: Gromacs <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:224940.85000.qm@web95411.mail.in2.yahoo.com">224940.85000.qm@web95411.mail.in2.yahoo.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>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 <a href="http://effect.ac/" target="_blank">effect.ac</a> anyone pls tell me how to install Grace in Fedora of Redhat?<br>
thanking you all<br>Shamik<br><br><br><br> See the Web&#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. <a href="http://in.buzz.yahoo.com/" target="_blank">http://in.buzz.yahoo.com/</a><br>
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<br>------------------------------<br><br>Message: 2<br>Date: Mon, 27 Jul 2009 14:28:31 +0300<br>From: Jussi Lehtola <<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>><br>Subject: Re: [gmx-users] GHrace install<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:1248694111.5152.2.camel@hawking.theorphys.helsinki.fi">1248694111.5152.2.camel@hawking.theorphys.helsinki.fi</a>><br>
Content-Type: text/plain<br><br>On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote:<br>> hi alli'm facing alot of trouble in installing grace in my redhat<br>> machine. its always complaining about Motiff API.. ive installed<br>
> Lesstiff but even afetr that grace is not getting installed....i can't<br>> make out how to install it? is there any problem in the path? should<br>> i've to set path before grace install. i've gone through several pages<br>
> about grace installation but with no <a href="http://effect.ac/" target="_blank">effect.ac</a> anyone pls tell me how<br>> to install Grace in Fedora of Redhat?<br><br>You should avoid compiling software yourself, because that beats the<br>
whole idea of having a) a distribution that has ready-to-use software<br>and b) a package management system that makes upgrades possible.<br><br>In Fedora<br># yum -y install grace<br><br>In RHEL, first enable the Fedora EPEL repository with<br>
# rpm -Uvh \<br><a href="http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm" target="_blank">http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm</a><br>and then install grace with<br>
# yum -y install grace<br><br>Then you can run grace with $ xmgrace<br>--<br>------------------------------------------------------<br>Jussi Lehtola, FM, Tohtorikoulutettava<br>Fysiikan laitos, Helsingin Yliopisto<br><a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>, p. 191 50632<br>
------------------------------------------------------<br>Mr. Jussi Lehtola, M. Sc., Doctoral Student<br>Department of Physics, University of Helsinki, Finland<br><a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a><br>
------------------------------------------------------<br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 27 Jul 2009 21:56:08 +0800<br>From: Lee Soin <<a href="mailto:nomadoro@gmail.com">nomadoro@gmail.com</a>><br>
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for<br> pairs of energy groups<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br> <<a href="mailto:e2838e4e0907270656n4be59b34w4488a610fefd4299@mail.gmail.com">e2838e4e0907270656n4be59b34w4488a610fefd4299@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br>
<br>I see in the .top file generated by pdb2gmx:<br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br><br>The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do<br>
c2 and c3 parametrize electrostatic interactions? And what do they stand for<br>respectively? Thanks!<br><br><br>2009/7/27 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br><br>> Lee Soin wrote:<br>
><br>>> My problem is actually as follows:<br>>><br>><br>> Please describe in as full detail as reasonable the first time :-)<br>><br>> I have three groups of atoms: A, B and C. Now I want to keep full<br>
>> interaction between A-B and A-C, but only retain the repulsive part of VDW<br>>> interaction between B-C. I'm using the OPLS force field. It seems to me<br>>> that<br>>> the parameters for OPLS in the .itp files are specified for each atom, so<br>
>> is<br>>> there any way to treat the interaction pairwise?<br>>><br>><br>> Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That<br>> will be tedious if there are many such atoms. Read parts of chapter 5.<br>
><br>> Probably, no force field was parameterized to reproduce whatever it is<br>> you're trying to observe.<br>><br>><br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br><br><br><br>--<br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a579dfe1/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a579dfe1/attachment-0001.html</a><br>
<br>------------------------------<br><br>Message: 4<br>Date: Mon, 27 Jul 2009 10:44:33 -0400<br>From: "jimkress_58" <<a href="mailto:jimkress_58@kressworks.org">jimkress_58@kressworks.org</a>><br>Subject: RE: [gmx-users] GHrace install<br>
To: "'Discussion list for GROMACS users'" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <D3E11AB6F6DC42AA8891734A1EF5BE9E@libraryPC><br>Content-Type: text/plain; charset="us-ascii"<br>
<br>If you are using a vanilla RedHat system, the yum method will work.<br>However, if you are using a prepackaged clustering environment (like ROCKS)<br>you may break it.<br><br>All you nee to know to install grace is the location of the headers and<br>
libraries for Lesstiff. You then supply them to grace as a part of the<br>./configure command and things should go smoothly.<br><br>It's unfortunate the person who wrote and maintains grace is unwilling to<br>provide this information to the people that want to use grace. However, you<br>
can't stop people from being jerks. That's why I'd prefer gromacs use a<br>different plotting package like gnuplot.<br><br>Jim<br><br>-----Original Message-----<br>From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>
On Behalf Of Samik Bhattacharya<br>Sent: Monday, July 27, 2009 7:19 AM<br>To: Gromacs<br>Subject: [gmx-users] GHrace install<br><br>hi alli'm facing alot of trouble in installing grace in my redhat machine.<br>its always complaining about Motiff API.. ive installed Lesstiff but even<br>
afetr that grace is not getting installed....i can't make out how to install<br>it? is there any problem in the path? should i've to set path before grace<br>install. i've gone through several pages about grace installation but with<br>
no <a href="http://effect.ac/" target="_blank">effect.ac</a> anyone pls tell me how to install Grace in Fedora of Redhat?<br>thanking you all<br>Shamik<br><br><br>________________________________<br><br>Looking for local information? Find it on Yahoo! Local<br>
<<a href="http://in.rd.yahoo.com/tagline_local_1/*http://in.local.yahoo.com/" target="_blank">http://in.rd.yahoo.com/tagline_local_1/*http://in.local.yahoo.com/</a>><br><br><br><br>------------------------------<br>
<br>Message: 5<br>Date: Mon, 27 Jul 2009 16:05:37 +0200 (CEST)<br>From: "Morteza Khabiri" <<a href="mailto:khabiri@greentech.cz">khabiri@greentech.cz</a>><br>Subject: [gmx-users] POSITION-RESTRAIN<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br> <<a href="mailto:21935.160.217.215.149.1248703537.squirrel@www.greentech.cz">21935.160.217.215.149.1248703537.squirrel@www.greentech.cz</a>><br>Content-Type: text/plain;charset=iso-8859-2<br><br>
Dear gmxusers.<br><br>I want to restrain the lipids in my system which contains protein,lipid<br>and water. I make the restraint itp file by genpr then I added it in<br>toplogy file.<br>After doing grompp to make tpr file I get the following message:<br>
<br>Fatal error:<br>[ file "posre_entirelipid1.itp", line 56 ]:<br> Atom index (53) in position_restraints out of bounds (1-52)<br>I found the similar error in the mailing list and they suggested probably<br>
the place of restraint itp file which was included in topology file is<br>wrong. However, I tried several positions for restraint itp but I think<br>it is not the<br>solution. Do you have any other suggestion about this problem??????<br>
<br>Thanks<br><br><br><br><br><br>------------------------------<br><br>Message: 6<br>Date: Tue, 28 Jul 2009 01:04:51 +1000<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] POSITION-RESTRAIN<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4A6DC213.1000700@anu.edu.au">4A6DC213.1000700@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-2; format=flowed<br><br>Morteza Khabiri wrote:<br>> Dear gmxusers.<br>><br>> I want to restrain the lipids in my system which contains protein,lipid<br>> and water. I make the restraint itp file by genpr then I added it in<br>
> toplogy file.<br>> After doing grompp to make tpr file I get the following message:<br>><br>> Fatal error:<br>> [ file "posre_entirelipid1.itp", line 56 ]:<br>> Atom index (53) in position_restraints out of bounds (1-52)<br>
> I found the similar error in the mailing list and they suggested probably<br>> the place of restraint itp file which was included in topology file is<br>> wrong. However, I tried several positions for restraint itp but I think<br>
> it is not the<br>> solution. Do you have any other suggestion about this problem??????<br><br>You're using a [ position_restraints ] directive that requires at least<br>53 atoms in a position where only 52 are defined. There are various<br>
explanations, including #including in the wrong place, or #including a<br>wrong file. Look carefully at a correct example.<br><br>Mark<br><br><br>------------------------------<br><br>Message: 7<br>Date: Tue, 28 Jul 2009 01:06:30 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] GHrace install<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4A6DC276.8050001@anu.edu.au">4A6DC276.8050001@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>jimkress_58 wrote:<br>> If you are using a vanilla RedHat system, the yum method will work.<br>
> However, if you are using a prepackaged clustering environment (like ROCKS)<br>> you may break it.<br>><br>> All you nee to know to install grace is the location of the headers and<br>> libraries for Lesstiff. You then supply them to grace as a part of the<br>
> ./configure command and things should go smoothly.<br>><br>> It's unfortunate the person who wrote and maintains grace is unwilling to<br>> provide this information to the people that want to use grace. However, you<br>
> can't stop people from being jerks. That's why I'd prefer gromacs use a<br>> different plotting package like gnuplot.<br><br>Agreed, although it is straightforward to use gnuplot anyway. See<br><a href="http://oldwiki.gromacs.org/index.php/Graphing_Data" target="_blank">http://oldwiki.gromacs.org/index.php/Graphing_Data</a><br>
<br>Mark<br><br><br>------------------------------<br><br>Message: 8<br>Date: Tue, 28 Jul 2009 01:10:53 +1000<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] About exclusion of non-bonded interaction for<br>
pairs of energy groups<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4A6DC37D.6020407@anu.edu.au">4A6DC37D.6020407@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Lee Soin wrote:<br>> I see in the .top file generated by pdb2gmx:<br>> [ pairs ]<br>> ; ai aj funct c0 c1 c2 c3<br>
><br>> The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do<br>> c2 and c3 parametrize electrostatic interactions? And what do they stand for<br>> respectively? Thanks!<br><br>No, they're two pairs of VDW parameters, one pair each for two possible<br>
states for a free-energy calculation. The tables in chapter 5 imply<br>this, but it is not at all obvious to a newcomer.<br><br>>> Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That<br>>> will be tedious if there are many such atoms. Read parts of chapter 5.<br>
<br>You should still do this.<br><br>Mark<br><br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<br>End of gmx-users Digest, Vol 63, Issue 131<br>******************************************<br></blockquote></div><br><br clear="all">
<div></div><br>-- <br>Prof. Dr. Luis Paulo Scott<br>CMCC- Centro de Matemática, Computação e Cognição<br>Universidade Federal do ABC<br>Grupo de Pesquisa em Biologia Computacional<br><br>