Re: [gmx-users] Coordinate file does not match topology
On 6/11/2007 4:27 AM, David van der Spoel wrote: Sheyore Omovie wrote: Thanks Yang, Each of the residues in my *.gro have more H-atoms than in *.top. I added the 21 H-atoms in [molecules] section of *.top. But grompp still came up with the ff error: No such molecule type. Do i have to edit [moleculetype] section too? Rgds John Please do not edit the topology file unless you are very sure what you are doing. You probably select a united atom force field and want to combine it with an all atom coordinate file. You will have to use the conf.gro that pdb2gmx produces. Hi, Omovie Hope David's comment help you to understand what you are doing with the step of grompp. No individual H-atom shall exist outside a molecule as we are not doing nuclear simulation. =) Regards, Yang Ye ___ 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] genion
What actually is it that you want to know about? Your email doesn't really specify anything that you are trying to find out. Are you wanting to maybe be able to neutralise the change in a system using genion? Have you looked at the tutorials and checked "genion -h"? -Original Message- From: [EMAIL PROTECTED] on behalf of Elias santos Sent: Sun 6/10/2007 4:21 AM To: gmx-users@gromacs.org Subject: [gmx-users] genion Hi!! I want know because we must neutralize the total load of the system (protein + water) in the interior of the box with genion. Elias <>___ 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] Coordinate file does not match topology
Sheyore Omovie wrote: Thanks Yang, Each of the residues in my *.gro have more H-atoms than in *.top. I added the 21 H-atoms in [molecules] section of *.top. But grompp still came up with the ff error: No such molecule type. Do i have to edit [moleculetype] section too? Rgds John Please do not edit the topology file unless you are very sure what you are doing. You probably select a united atom force field and want to combine it with an all atom coordinate file. You will have to use the conf.gro that pdb2gmx produces. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Coordinate file does not match topology
Thanks Yang, Each of the residues in my *.gro have more H-atoms than in *.top. I added the 21 H-atoms in [molecules] section of *.top. But grompp still came up with the ff error: No such molecule type. Do i have to edit [moleculetype] section too? Rgds John From: Yang Ye <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Sun, 10 Jun 2007 23:02:29 +0800 On 6/10/2007 8:54 PM, Sheyore Omovie wrote: You're right, the total charge is zero. While creating *.top, pdb2gmx did not recognise some hydrogen atoms in my pdb file (HA atom type in particular). I had to use -ignh to ignore the H-atoms. No. This is not the reason why there are different number of atoms inside your .gro and .top. pdb2gmx shall always generate a correct top. Can I just add this atoms to the *.top like u've stated below, or do I need to edit *.rtp to include this particular H-atom. Check other steps. Or check what's the difference (which type of molecule has more number) if you want to find the root of the problem? Or just proceed with my suggested modification. Rgds John From: Yang Ye <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Sun, 10 Jun 2007 20:00:47 +0800 There is 2312-2291=21 more atoms in your structure file than in the topology file. If it is due to genion, it shall be less. There might be other mistakes in previous steps. Anyway, to make them match, just count how many molecules you have in the system. The last section in your top file shall be something like [ molecules ] Protein X SOL X K+ X Match the number there. Commands like grep SOL ABC.gro | wc or grep Mg ABC.gro | wc or grep POT ABC.gro | wc shall be your good companion. Regards, Yang Ye On 6/10/2007 8:42 AM, Sheyore Omovie wrote: Thanks, But this is my first real simulation, So I'll appreciate it if you can tell me how to determine the number of ions to add with genion. Thanks John From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT) Small errors like that are usually down to things like running genion and not changing the .top. I think I made a problem for myself once with non-consecutive atom numbering, too. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files with grompp, i got the ff error > message: > "Number of coordinates in coordinate file (b4em.gro, 2312) does not > match topology (twopolypeptide.top, 2291)" > How can I fix this? Make them match. Assuming you haven't managed a gross mismatch of files, your [molecules] section of your .top probably isn't right. Chapter five of the manual is your friend 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 The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.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 _ Make every IM count. Download Messenger and join the im Initiative now. Its free. http://im.live.com/messenger/im/home/?source=TAGHM_June07 ___ 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/
Re: [gmx-users] tpbconv restart crashing on 3.3.1
Alan Dodd wrote: Hello all, A recent simulation has been running on a cluster for a couple of weeks. 5.something-ns in it crashed due to a hardware glitch. All perfectly understandable so far. The strange thing is, using tpbconv now results in a .tpr that crashes in the first step due to massive LINCS errors. Even if you use the option -time to take the simulation way back, to say 0.5ns when it ought to still be fine, it still crashes. Other simulations on the same hardware+software are running fine, other restarts from other jobs crashing at the same time have worked fine, so it doesn't look like a bug. Any suggestions as to why LINCS errors could suddenly now prevent the simulation from running *any* of the steps that it previously ran just fine? I just want a hint as to what we could have missed, really. Alan Dodd UoB Did you give tpbconv the energy file as well? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Coordinate file does not match topology
On 6/10/2007 8:54 PM, Sheyore Omovie wrote: You're right, the total charge is zero. While creating *.top, pdb2gmx did not recognise some hydrogen atoms in my pdb file (HA atom type in particular). I had to use -ignh to ignore the H-atoms. No. This is not the reason why there are different number of atoms inside your .gro and .top. pdb2gmx shall always generate a correct top. Can I just add this atoms to the *.top like u've stated below, or do I need to edit *.rtp to include this particular H-atom. Check other steps. Or check what's the difference (which type of molecule has more number) if you want to find the root of the problem? Or just proceed with my suggested modification. Rgds John From: Yang Ye <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Sun, 10 Jun 2007 20:00:47 +0800 There is 2312-2291=21 more atoms in your structure file than in the topology file. If it is due to genion, it shall be less. There might be other mistakes in previous steps. Anyway, to make them match, just count how many molecules you have in the system. The last section in your top file shall be something like [ molecules ] Protein X SOL X K+ X Match the number there. Commands like grep SOL ABC.gro | wc or grep Mg ABC.gro | wc or grep POT ABC.gro | wc shall be your good companion. Regards, Yang Ye On 6/10/2007 8:42 AM, Sheyore Omovie wrote: Thanks, But this is my first real simulation, So I'll appreciate it if you can tell me how to determine the number of ions to add with genion. Thanks John From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT) Small errors like that are usually down to things like running genion and not changing the .top. I think I made a problem for myself once with non-consecutive atom numbering, too. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files with grompp, i got the ff error > message: > "Number of coordinates in coordinate file (b4em.gro, 2312) does not > match topology (twopolypeptide.top, 2291)" > How can I fix this? Make them match. Assuming you haven't managed a gross mismatch of files, your [molecules] section of your .top probably isn't right. Chapter five of the manual is your friend 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 The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.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 _ Make every IM count. Download Messenger and join the i?m Initiative now. It?s free. http://im.live.com/messenger/im/home/?source=TAGHM_June07 ___ 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 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 _ Don?t miss your chance to WIN $10,000 and other great prizes from Microsoft Office Live http://clk.atdmt.com/MRT/go/aub0540003042mrt/direct/01/
[gmx-users] Re: generating a top file
Hi, Saf We use a special bond for heme, specified in specbond.dat. Check the mailing list archive. Regards, Yang Ye On 6/10/2007 9:17 PM, Shahrokh Safarian wrote: Dear Yang YE Thank you very much for your kind cooperation. I did upload my pdb file to prodrg but there were two problems: 1) the size of the file was high 2) there was an Fe atom which was not supported by prodrg In fact I am trying to simulate an iron containing enzyme which dose not contained of a typical heme group. So, as you know, if we want to have a good simulation, the Fe3+ ion should be covalently bounded to the nitrogen atoms of at least two or three His residues until the ion has not been moved from its initial location in the molecule. Did hoy have any similar experience before and could you lead me to solve this problem? Thanks saf ___ 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] Coordinate file does not match topology
You're right, the total charge is zero. While creating *.top, pdb2gmx did not recognise some hydrogen atoms in my pdb file (HA atom type in particular). I had to use -ignh to ignore the H-atoms. Can I just add this atoms to the *.top like u've stated below, or do I need to edit *.rtp to include this particular H-atom. Rgds John From: Yang Ye <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Sun, 10 Jun 2007 20:00:47 +0800 There is 2312-2291=21 more atoms in your structure file than in the topology file. If it is due to genion, it shall be less. There might be other mistakes in previous steps. Anyway, to make them match, just count how many molecules you have in the system. The last section in your top file shall be something like [ molecules ] Protein X SOL X K+ X Match the number there. Commands like grep SOL ABC.gro | wc or grep Mg ABC.gro | wc or grep POT ABC.gro | wc shall be your good companion. Regards, Yang Ye On 6/10/2007 8:42 AM, Sheyore Omovie wrote: Thanks, But this is my first real simulation, So I'll appreciate it if you can tell me how to determine the number of ions to add with genion. Thanks John From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT) Small errors like that are usually down to things like running genion and not changing the .top. I think I made a problem for myself once with non-consecutive atom numbering, too. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files with grompp, i got the ff error > message: > "Number of coordinates in coordinate file (b4em.gro, 2312) does not > match topology (twopolypeptide.top, 2291)" > How can I fix this? Make them match. Assuming you haven't managed a gross mismatch of files, your [molecules] section of your .top probably isn't right. Chapter five of the manual is your friend 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 The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.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 _ Make every IM count. Download Messenger and join the im Initiative now. Its free. http://im.live.com/messenger/im/home/?source=TAGHM_June07 ___ 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 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 _ Dont miss your chance to WIN $10,000 and other great prizes from Microsoft Office Live http://clk.atdmt.com/MRT/go/aub0540003042mrt/direct/01/ ___ 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.p
Re: [gmx-users] generating a top file
This is called parameterization. http://wiki.gromacs.org/index.php/Parameterization For small molecule, you can opt for PRODRG for GROMOS/GROMACS force fields; or Antechamber for AMBER force field. Once you obtained the topology, convert them back to the format in the rtp file according to the manual. Regards, Yang Ye On 6/10/2007 7:28 PM, Shahrokh Safarian wrote: Dear colleagues As you know if we want to introduce a new molecule into Gromacs, the related parameters for that molecule (e.g. [atoms], [bonds], [pairs], [dihedrals] and so on) should be inserted to the Gromacs rtp file. In the Gromacs user's manual (page 100) an example for these types of topology parameters is propounded for urea molecule. The main question is how can we obtain these topology parameters for a desired molecule? regards saf ___ 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 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] generating a top file
Dear colleagues As you know if we want to introduce a new molecule into Gromacs, the related parameters for that molecule (e.g. [atoms], [bonds], [pairs], [dihedrals] and so on) should be inserted to the Gromacs rtp file. In the Gromacs user's manual (page 100) an example for these types of topology parameters is propounded for urea molecule. The main question is how can we obtain these topology parameters for a desired molecule? regards saf ___ 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] Coordinate file does not match topology
There is 2312-2291=21 more atoms in your structure file than in the topology file. If it is due to genion, it shall be less. There might be other mistakes in previous steps. Anyway, to make them match, just count how many molecules you have in the system. The last section in your top file shall be something like [ molecules ] Protein X SOL X K+ X Match the number there. Commands like grep SOL ABC.gro | wc or grep Mg ABC.gro | wc or grep POT ABC.gro | wc shall be your good companion. Regards, Yang Ye On 6/10/2007 8:42 AM, Sheyore Omovie wrote: Thanks, But this is my first real simulation, So I'll appreciate it if you can tell me how to determine the number of ions to add with genion. Thanks John From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Coordinate file does not match topology Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT) Small errors like that are usually down to things like running genion and not changing the .top. I think I made a problem for myself once with non-consecutive atom numbering, too. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files with grompp, i got the ff error > message: > "Number of coordinates in coordinate file (b4em.gro, 2312) does not > match topology (twopolypeptide.top, 2291)" > How can I fix this? Make them match. Assuming you haven't managed a gross mismatch of files, your [molecules] section of your .top probably isn't right. Chapter five of the manual is your friend 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 The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.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 _ Make every IM count. Download Messenger and join the i?m Initiative now. It?s free. http://im.live.com/messenger/im/home/?source=TAGHM_June07 ___ 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 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] position by editconf
mahbubeh zarrabi wrote: dear all I want to insert protein in bilayer. how can i put position of protein in x,y, and z ralative to the bilayer by editconf? best regards editconf -h No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] position by editconf
dear all I want to insert protein in bilayer. how can i put position of protein in x,y, and z ralative to the bilayer by editconf? best regards No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail ___ 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
