[gmx-users] problem with structure factor in g_rdf
Hi, I was trying to use g_rdf analysis tool to calculate the structure factor of a polymer I am simulating. I have generated own ..itp files for the polymer and the simulation is going ok. But, whenever, I am trying to use g_rdf tool to calculate the structure factor, it returns the following error: Reading frames from gro file '', 89600 atoms. Reading frame 0 time0.000 --- Program g_rdf, VERSION 3.3.1 Source code file: gmx_rdf.c, line: 819 Fatal error: Error: atom type (NH3) not in list (18 types checked)! The command line I am using is as follows: g_rdf -f conf.gro -n index.ndx -o rdf2.xvg -sq sq.xvg -s topol.tpr If I only try to calculate the rdf, it goes fine. But only when I am using -sq option , I am getting the error. I checked with gromacs mailing list and I saw an email having similar problem as mine but I did not find any solution. It will be great, if any one can help me with this problem. Thanks Jagannath Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.messenger.yahoo.com/webmessengerpromo.php/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: [gmx-use rs] about using amb2gmx.pl
Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? Regards! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sir : Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore! Your use of terminology is unclear - and you can't afford this sort of lack of clarity in science. pdb, gro and top are all generic file formats. Your first email implied that you did have a file with your initial coordinates. The above implies the opposite. If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. I'd also suggest you follow Justin's advice, and do some tutorial material. If nothing else they should teach you by example some better ways of describing these things! :) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] distance options for g_cluster
OZGE ENGIN wrote: Hi all, I am trying to understand what type of distance can be used with g_cluster? In the manual, it is written that RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph. However, in the other options part, two options are indicated for -dista option, which indicates the type of distance that will be used with g_cluster. They are RMSD of distances or RMS deviation. Consequently, the information in the first paragraph does not coincide with that given in the other options part for -dista option. Maybe I could not understand. Could anyone explain this in a clearer way, please? I agree that it is not very clear what is meant in the documentation, and I have wondered myself what it means. This is one of the reasons that the source code is made available. I had a quick look, and -dista yes looks like it implements the RMS deviation of atom-pair distances quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those matrices to generate the structure comparison matrix for clustering. You'd be well advised to verify that yourself. It's all in src/tools/gmx_cluster.c Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： Re: 回复： Re: [gmx-users] abo ut using amb2gmx.pl
xi zhao wrote: Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. It sounds like my earlier advice is appropriate. If you need to insert your chromophore into your protein to form a complex to give yourself an initial structure, then you will need to choose that protein structure in a suitable conformation (this is not trivial) and then to dock that chromophore. How easy it is to do the latter will depend on your available experimental information. Google (or scientific literature) searching for docking and model building is your best bet here - it's well outside the scope of the GROMACS tool set. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: [gmx-users] about using amb2gmx.pl
Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. It sounds like my earlier advice is appropriate. If you need to insert your chromophore into your protein to form a complex to give yourself an initial structure, then you will need to choose that protein structure in a suitable conformation (this is not trivial) and then to dock that chromophore. How easy it is to do the latter will depend on your available experimental information. Google (or scientific literature) searching for docking and model building is your best bet here - it's well outside the scope of the GROMACS tool set. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： Re: 回复： Re: 回复： Re: [gmx -users] about using amb2gmx.pl
xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: 回复： Re: [gmx-users] ab out using amb2gmx.pl
Dear sir: Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl
Dear sir : In fact, PRODRG can not produce chromophore top files properly, so I have to give up gromos force field! The normal force field does not have params about chromophore. Justin A. Lemkul [EMAIL PROTECTED] 写道： Search for John Kerrigan's enzyme-ligand tutorial. It explains in clear detail everything you will need to do. Ignore the part about using PRODRG for your chromophore, as you apparently already have this information from antechamber. For the future, it would be more clear to post this type of information: 1. What structures (pdb/gro, doesn't really matter) you already have 2. What topologies you have, and how you generated them 3. Specific errors you are having (from pdb2gmx, etc), not simply I cannot get top and gro for the whole complex. It leaves us wondering what you have or haven't tried doing. -Justin Quoting xi zhao : Dear sir: Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Mark Abraham 写道： xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: »Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: [gmx-users] about using amb2gmx.pl
Search for John Kerrigan's enzyme-ligand tutorial. It explains in clear detail everything you will need to do. Ignore the part about using PRODRG for your chromophore, as you apparently already have this information from antechamber. For the future, it would be more clear to post this type of information: 1. What structures (pdb/gro, doesn't really matter) you already have 2. What topologies you have, and how you generated them 3. Specific errors you are having (from pdb2gmx, etc), not simply I cannot get top and gro for the whole complex. It leaves us wondering what you have or haven't tried doing. -Justin Quoting xi zhao [EMAIL PROTECTED]: Dear sir: Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Mark Abraham [EMAIL PROTECTED] дµÀ£º xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - ÑÅ»¢ÓÊÏä´«µÝÐÂÄê×£¸££¬¸öÐԺؿ¨ËÍÇ×Åó£¡ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： Re: 回复： Re: 回复： Re: 回复 ： Re: 回复� Re: [gmx-users] about using amb2 gmx.pl
xi zhao wrote: Dear sir : In fact, PRODRG can not produce chromophore top files properly, so I have to give up gromos force field! The normal force field does not have params about chromophore. See http://wiki.gromacs.org/index.php/Exotic_Species Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] distance options for g_cluster
Thank you Mark for your feedbacks. There is one more point that is not clear to me for the output of g_cluster, In the second column of the cluster.log of g_cluster, the same rmsd values are indicated for different clusters. What does it mean? Although these clusters have the same cut-off value, they are grouped in different clusters, Why? Thank you. -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 17 Feb 2008 22:35:20 +1100 Subject: Re: [gmx-users] distance options for g_cluster OZGE ENGIN wrote: Hi all, I am trying to understand what type of distance can be used with g_cluster? In the manual, it is written that RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph. However, in the other options part, two options are indicated for -dista option, which indicates the type of distance that will be used with g_cluster. They are RMSD of distances or RMS deviation. Consequently, the information in the first paragraph does not coincide with that given in the other options part for -dista option. Maybe I could not understand. Could anyone explain this in a clearer way, please? I agree that it is not very clear what is meant in the documentation, and I have wondered myself what it means. This is one of the reasons that the source code is made available. I had a quick look, and -dista yes looks like it implements the RMS deviation of atom-pair distances quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those matrices to generate the structure comparison matrix for clustering. You'd be well advised to verify that yourself. It's all in src/tools/gmx_cluster.c Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php is made available. I had a quick look, and -dista yes looks like it implements the RMS deviation of atom-pair distances quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Patch for PME in Free Energy?
Hi all, I guess this is directed towards the developers. Thanks to David Mobley, I was able to determine that my free energy calculations were victim of a PME bug in version 3.3.1. In the Bugzilla, Berk commented that the issue had been resolved for the upcoming release of versions 3.3.3 and 4.0, so I'm guessing the issue remains in version 3.3.2? If so, is there a modification I can make to any source code files (either version 3.3.1 or 3.3.2) so I can re-compile, or should I just be patient and wait for version 3.3.3? Thanks, Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polyethylene
Dear GMX users, I want to prepare .gro and topology files starting from the .pdb file for a polyethylene chain , whose residue is not defined in .rtp, .hdb. and .tdb files. I have defined a new residue in ffoplsaa.rtp file as follows [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 In ffoplsaa.hdb I defined it as Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 At this point I have to note that the presence of the last control atoms in this file has not influenced the process. In ffoplsaa-n.tdb file I have added [ Eth ] [ replace ] C2 opls_13512.011 -0.18 [ add ] 34 H2 C2 C1 opls_140 1.008 0.06 [ delete ] H21 H22 and in ffoplsaa-c.tdb file I have added [ Eth ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H11 H12 After using pdb2gmx -f input.pdb I have obtained following message Opening library file ffoplsaa.rtp Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 6 atoms chain #res #atoms 1 ' ' 3 6 All occupancies are one Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Residue 59 Sorting it all out... Opening library file ffoplsaa.hdb Error in hdb file: nah = 41 line = '' Opening library file ffoplsaa-n.tdb Opening library file ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.8# Processing chain 1 (6 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: Eth C-terminus: Eth Segmentation fault Could you specify what means Error in hdb file: nah = 41 line = '' and what is the problem with segmentation. My input structure in .pdb file is as follows ATOM 1 C1 Eth 1 1.000 1.540 0.000 ATOM 2 C2 Eth 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 Eth 3 3.912 5.623 0.000 ATOM 6 C2 Eth 3 5.368 6.124 0.000 END Thank you for help in advance Best regards Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Patch for PME in Free Energy?
Hi Justin, I can understand that you want your forward and reverse direction results to be equal for verification reasons. But keep in mind that there really is no forward or reverse direction when doing TI on separately equilibrated (i.e. independent for every lambda) starting stuctures (which is IMHO the right way do do TI, btw). There is no physical reason to check whether both directions give equal results; a simulation for lambda=0.35 in the forward direction is (or should be) exactly equivalent to a simulation for lambda=0.65 in the reverse direction, except for the sign of d(lambda). There is only a computational reason, obviously, since it helps finding code bugs. ;-) So if the forward direction is working fine (which I believe it is), than you don't really need this patch. Simply make sure that your topologies are consistently defined in that direction. Having said that, and taking my first sentence into account, you could try downloading the 3.3 CVS version. From the information Berk has given in bug 175, I'm guessing the code was changed somewhere in pme.c, nb_free_energy.c or force.c. So you may want to 'diff' those with the 3.3.1 files and alter them accordingly. But since I'm not an expert on the code, I could be wrong about the files. Cheers, Jeroen Date: Sun, 17 Feb 2008 17:12:57 -0500 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: [gmx-users] Patch for PME in Free Energy? To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi all, I guess this is directed towards the developers. Thanks to David Mobley, I was able to determine that my free energy calculations were victim of a PME bug in version 3.3.1. In the Bugzilla, Berk commented that the issue had been resolved for the upcoming release of versions 3.3.3 and 4.0, so I'm guessing the issue remains in version 3.3.2? If so, is there a modification I can make to any source code files (either version 3.3.1 or 3.3.2) so I can re-compile, or should I just be patient and wait for version 3.3.3? Thanks, Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Stanford workshop april 7-8
Hi Ozge, Not yet, since we came up with the idea during biophysical society, but with a bit of luck it should be already this fall! Cheers, Erik On Feb 16, 2008, at 9:40 AM, OZGE ENGIN wrote: Hi Erik, Did you put up a registration page for the workshop? Could you give information, if there is any, about the workshop that will be held in Göttingen? I am outside of the countries you mentioned :) -Original Message- From: Erik Lindahl [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 15 Feb 2008 20:13:19 +0100 Subject: [gmx-users] Stanford workshop april 7-8 Hi again, Quick update: I've finally settled the block room reservations at the guest house ($89 for singles, $119 for doubles), and will try to put up a registration page in a couple of hours. I think I have a solution to keep it reasonably fair just in case there's overwhelming interest: In the first round I'll simply let everybody register until tuesday night (PST) next week, and if by then there are more people than slots (~30) we will have to draw randomly, but give people from US/Canada/ Mexico priority. Hopefully Europeans will get another chance in Göttingen soon :-) From wednesday any possible remaining slots will be filled on a first- come, first-served, basis. Cheers, Erik Erik Lindahl [EMAIL PROTECTED] Backup: [EMAIL PROTECTED] Assistant Professor, Computational Structural Biology Center for Biomembrane Research, Dept. Biochemistry Biophysics Stockholm University, SE-106 91 Stockholm, Sweden Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Erik Lindahl [EMAIL PROTECTED] Backup: [EMAIL PROTECTED] Assistant Professor, Computational Structural Biology Center for Biomembrane Research, Dept. Biochemistry Biophysics Stockholm University, SE-106 91 Stockholm, Sweden Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: Patch for PME in Free Energy?
Thanks for the input and useful information, Jeroen. I am trying to parameterize some new molecules for use in my future work, so I would like to take as much care as possible in getting things right! -Justin Quoting van Bemmelen [EMAIL PROTECTED]: Hi Justin, I can understand that you want your forward and reverse direction results to be equal for verification reasons. But keep in mind that there really is no forward or reverse direction when doing TI on separately equilibrated (i.e. independent for every lambda) starting stuctures (which is IMHO the right way do do TI, btw). There is no physical reason to check whether both directions give equal results; a simulation for lambda=0.35 in the forward direction is (or should be) exactly equivalent to a simulation for lambda=0.65 in the reverse direction, except for the sign of d(lambda). There is only a computational reason, obviously, since it helps finding code bugs. ;-) So if the forward direction is working fine (which I believe it is), than you don't really need this patch. Simply make sure that your topologies are consistently defined in that direction. Having said that, and taking my first sentence into account, you could try downloading the 3.3 CVS version. From the information Berk has given in bug 175, I'm guessing the code was changed somewhere in pme.c, nb_free_energy.c or force.c. So you may want to 'diff' those with the 3.3.1 files and alter them accordingly. But since I'm not an expert on the code, I could be wrong about the files. Cheers, Jeroen Date: Sun, 17 Feb 2008 17:12:57 -0500 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: [gmx-users] Patch for PME in Free Energy? To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi all, I guess this is directed towards the developers. Thanks to David Mobley, I was able to determine that my free energy calculations were victim of a PME bug in version 3.3.1. In the Bugzilla, Berk commented that the issue had been resolved for the upcoming release of versions 3.3.3 and 4.0, so I'm guessing the issue remains in version 3.3.2? If so, is there a modification I can make to any source code files (either version 3.3.1 or 3.3.2) so I can re-compile, or should I just be patient and wait for version 3.3.3? Thanks, Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Loss of GTP in topology file.
s lal badshah wrote: Hi, I have added missing atoms to my pdb file through servers of WHATIF,when I use the force field option then the following output comes in shell console: Fatal error: Residue 'GTP' not found in residue topology database and the following files are created: 2a5f.top 2a5f_A.itp 2a5f_B.itp posre_A.itp posre_B.itp Please describe what you're doing here, with actual console input. If you were using pdb2gmx and got this fatal error, then there these .top and .itp files will not have been created by pdb2gmx. See http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database for discussion of this pdb2gmx error message. Please guide me so that GTP is added to PDB.Further which force field and box will be better for my simulation of enzyme-Protein GTP complex? This is not a simple question, and you need to search the literature thoroughly to see what other people have done for systems similar to yours and consider their reasons. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Registration open for Stanford workshop April 7 8
Hi, Oops - I happened to only post this to the gmx-developers list first: I have put up a somewhat primitive information registration page about the Stanford workshop at http://www.gromacs.org/stanford2008/ As I mentioned on friday, the space is somewhat limited (30-35 participants), so I will do the registration in two stages. 1) Through Tuesday February 20, anybody who registers will be part of the first round. If the workshop fills up already here I will select participants randomly, but give priority to contributors and participants from the US side of the pond. 2) From February 21, the second round it will be first-come, first- served. I will sent out confirmation letters to all accepted participants within a day, but not earlier than February 20! The group block reservation at the Stanford guest house is in place until March 6. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
