[gmx-users] g_hbond Issues
Dear Gmx Users, I need to calculate the H-Bonds of simulation trajectory with specification of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately. Do anyone have any idea how to do this...since the present option g_hbond calculate both the hydrogen bonds together irrespective of i to i+/- 2/3/4/5/6 and so on.. Or is there any other program which can be used for this analysis. Thanks in advance, With Regards, Anil Kumar IIT Bombay. India ___ gmx-users mailing listgmx-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
[gmx-users] Visit my Netlog profile
Hey, I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile. Take a look: http://en.netlog.com/go/mailurl/type=invite_1mailid=428030350id=1url=-L2dvL3JlZ2lzdGVyL2lkPTEyODg1OTc0MjkmaT10OTE_ Greetings, Anil Don't want to receive invitations from your friends anymore? http://en.netlog.com/go/mailurl/type=invite_1mailid=428030350id=2url=-L2dvL25vbWFpbHMvaW52aXRlL2VtYWlsPS1aMjE0TFhWelpYSnpRR2R5YjIxaFkzTXViM0puJmNvZGU9MTM0MTUyNjkmaWQ9MTI4ODU5NzQyOSZpPXQ5Mg__ ___ gmx-users mailing listgmx-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
[gmx-users] Invitation to connect on LinkedIn
LinkedIn Anil Kumar requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Anil View invitation from Anil Kumar http://www.linkedin.com/e/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/1112719262_2/0OnP8SczANdP8Ncj4LqnpPbOYWrSlI/svi/ -- Why might connecting with Anil Kumar be a good idea? People Anil Kumar knows can discover your profile: Connecting to Anil Kumar will attract the attention of LinkedIn users. See who's been viewing your profile: http://www.linkedin.com/e/wvp/inv18_wvmp/ -- (c) 2009, LinkedIn Corporation ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] regarding dimethylated lysine topology file
Dear Prasun, I think you can get the help of Chem 3D for fixing this problem. First you have to generate the topology with Chem 3D then get the gromacs format with PRODRG server of the same. I hope it will help you, with regards anil On Mon, Mar 2, 2009 at 2:21 PM, prasun kumar prasu...@gmail.com wrote: respected all I m tryin to generate a topology file for dimethylated lysine using PRODRG server,but I found that its not working...can you plz help me in gettin some another servers or any method... is it possible to change gromacs topology file to charmm topology file thanx in advance PRASUN (ASHOKA) ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- (¨`•.•´¨) Always `•.¸(¨`•.•´¨) Keep (¨`•.•´¨)¸.•´ Smiling! `•.¸.•´ «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•» «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•» ANIL KUMAR (Research Associate) C/O Prof. S. Durani Bio-Organic Lab No - 336 (2nd Floor), Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076 (INDIA) Ph. No.- +91-22-25764780 (Lab) - +91-22-25764168 (Lab) Mobile:- +91-9819638547 *** Web:http://chemanil.googlepages.com/ *** --- Time is money and duty is God.To rise in life , One must respect both ! ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Concentration of Urea in urea solvation box
As Peter has said you have to maintain the ratio of water molecule with respect to urea to get the desired concentration. So, in your case your system must have ratio of Water:Urea = 6.9375:1 (what i understood from the logic of calculation) for 8m Urea concentration (Plz note urea concentration is usually taken in molal not in molar..be careful!) You can start with the default urea+h2o.gro file of gromacs which has concentration of 6m...and do some editing according to your desired concentration followed by density adjustment and equilibrate it for sometime thats it. with regards -- (¨`•.•´¨) Always `•.¸(¨`•.•´¨) Keep (¨`•.•´¨)¸.•´ Smiling! `•.¸.•´ «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•» «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) Mobile:-09819638547 - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) --- Time is money and duty is God.To rise in life , you must respect both ! --- On Fri, Sep 5, 2008 at 1:23 AM, Nagy, Peter I. [EMAIL PROTECTED]wrote: Without an experiment you may not know the correct composition. 1 dm3 water contains 55.5 mol water. If you want to model a 8M urea solution, you should replace the correct number of the water molecules / 55.5 water. An urea (H2NCONH2 if I am not mistaken) contains 4 heavy atom. If you replace 8x4 water molecules by 8 urea in every 55.5 water subsystem, then you will have a good starting point. Then run an NpT job and check the volume. For example, if you start with 555 water molecules, replace 320 of them by 80 urea and so on. After an equilibration phase (1 ns or so) you will find a stable density, and see whether the density corresponds to 8M urea / 1dm3. Then you can make an estimate, how to modify the composition if necessary because of the too low or high concentration Peter Nagy University of Toledo -- *From:* [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] *Sent:* Thu 9/4/2008 2:51 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Concentration of Urea in urea solvation box Hi All, This is a trivial question. But I am quite puzzled about it, and I really need someone's kind help. I want to prepare 8M urea solution box, for which I might need to know input as number of water molecules and of urea. Now my query is how to make sure of these exact number of molecules. I know its really a basic question. One thing could be by experiment if we can make sure exact number of moles of water added to make molar solution. But i dont have any access to such wet lab things. So if anyone can help me out how to do these back end calculations. Another query is will the box size also play a role? Please be patient with this trivial query, but this simple calculation question is baffling me from quite a few days. Thanks in advance, Regards, Monika ___ 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 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] Fatal error: No such moleculetype Cl
Hi, You have not used the right command for adding the CL- ion to your system. Before adding/doing your simulation you must go through the manual and useful tutorial of John E. Kerrigan. Use genion command to add the charged ions. regards anil - (¨`•.•´¨) Always `•.¸(¨`•.•´¨) Keep (¨`•.•´¨)¸.•´ Smiling! `•.¸.•´ «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•» «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) Mobile:-09819638547 - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) --- Time is money and duty is God.To rise in life , you must respect both ! On Tue, May 6, 2008 at 1:17 PM, [EMAIL PROTECTED] wrote: Dear Users When I try adding charges (negative charges by adding Cl), using the command /opt/gromacs/bin/grompp_mpi -np 32 -f em_cc.mdp -po det_em2.mdp -c 1A92_m1_neu.gro -p 1A92_m1.top -o 1A92_m1_em.tpr it gives me the following error... --- Program grompp_mpi, VERSION 3.3.1 Source code file: toppush.c, line: 1293 Fatal error: No such moleculetype CL --- Could anyone tell me what would be the possible reason for this error? Thanks in advance Namitha Mohandas National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India ___ 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] Angle definition in g_hbond ...
Hi, Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly check how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30 in version 3.3.1, but in earlier version the angle cut-off was 60 in version 3.2 and 120 in version 3.1. regards anil IITB, India On Mon, May 5, 2008 at 7:20 PM, David van der Spoel [EMAIL PROTECTED] wrote: Mark Abraham wrote: sharada wrote: dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I plot the hydrogen bonds for some of the structures picked up through the dynamics using InsightII I am able to see the backbone HBs in almost all of them. This is the command I am using: g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num hnum.xvg -g hb.log this is the output I obtain and the hb.log file is not created : Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision) Specify 2 groups to analyze: Group 0 ( Protein) has 358 elements Group 1 ( Protein-H) has 271 elements Group 2 ( C-alpha) has36 elements Group 3 (Backbone) has 108 elements Group 4 ( MainChain) has 144 elements Group 5 (MainChain+Cb) has 177 elements Group 6 ( MainChain+H) has 181 elements Group 7 ( SideChain) has 177 elements Group 8 ( SideChain-H) has 126 elements Group 9 ( Prot-Masses) has 358 elements Select a group: 3 Selected 4: 'Backbone' Select a group: 3 Selected 4: 'Backbone' Calculating hydrogen bonds in Backbone (108 atoms) Found 0 donors and 72 acceptors No Donors found I haven't used this tool, but the problem looks like it is here. Are there any hydrogens in this group? use 6 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 -- (¨`•.•´¨) Always `•.¸(¨`•.•´¨) Keep (¨`•.•´¨)¸.•´ Smiling! `•.¸.•´ «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•» «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) Mobile:-09819638547 - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) --- Time is money and duty is God.To rise in life , you must respect both ! ___ 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] g_hbond (Version 3.3 vs Version 3.14)
Dear David, Thanks for your concern. i am using g_hbond (After vacuum md, just for one step) Command with options is g_hbond -f *.pdb -s *.tpr -num *_num.xvg -hx *_hbhelix.xvg and when i compare the result of v 3.3.1 and v 3.14, i found there is difference in *_hbhelix.xvg. Even for standard helix PDB of octa-alanine capped with ACE and NAC, v 3.3.1 is giving hydrogen bonds under n-n (Value is 3), n-n+1 (Value is 3) and rest is showing zero value. While on contrary v 3.1.4 is giving the correct answer with the value of 6 under the n-n+4. So, am i doing something wrong or is it bug in v 3.3.1! thanks in advance, With Regards anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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] g_hbond (Version 3.3 vs Version 3.14)
Dear All, I found there is some problem with version 3.3 to g_hbond command. Earlier i was using version 3.14, and when i was using g_hbond(v3.14) i found correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so on). But when i use g_hbond (v3.3) then i found it only gives hydrogen bonds between n-n, n-n+1,n-n+2 and rest will have value zero. Is it some bug to version 3.3 or am i doing mistake ! thanks in advance. Regards, anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: membranes proteins revisited (Alan Dodd) 2. Re: HELP REGARDING COMMAND g_pvd (Jochen Hub) 3. Re: Membrane protein simulation (Yanzi Zhou) 4. regarding range checking error and constraint errors in Lincs algorithm (shyamala iyer) 5. Re: regarding range checking error and constraint errorsin Lincs algorithm (Matt Wyczalkowski) -- Message: 1 Date: Wed, 19 Dec 2007 04:58:16 -0800 (PST) From: Alan Dodd [EMAIL PROTECTED] Subject: Re: [gmx-users] membranes proteins revisited To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Of course it's unnatural, it's a membrane made of gas instead of lipid ;) I'd recommend that you equilibrate the membrane first, and check it actually behaves in a manner close enough to one for what you want - and then insert a protein into it. You might want to look into the make_hole suite on the user contributions page, it's designed to make a hole in a lipid membrane for a protein, but I'm sure modifying it for argon would be rather trivial. - Original Message From: Magnus Andersson [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Tuesday, December 18, 2007 9:38:09 PM Subject: [gmx-users] membranes proteins revisited Hi all, I have a trimer membrane protein structure an artificial Argon grid membrane (100x100x30Å). First I wonder whether you should equilibrate the membrane first (it looks very un-natural, like a perfect grid...) and then physically remove atoms where I want to have my protein, then run: genbox -cp protein.gro -cs membrane.gro if I just run it as it is, I get: Checking Protein-Solvent overlap: tested 1512 pairs, removed 9261 atoms. I feel I'm getting there, but need some advice to come to the point where I have my trimer in a relaxed membrane... Thanks / Magnus -- Magnus Andersson Chalmers University of Technology Dept of Chemistry and Biological Engineering Email: [EMAIL PROTECTED] Homepage: http://www.csb.gu.se/neutze/ Phone: +46 (0)31-786 3917 Fax: +46 (0)31-786 3910 Lundberg Laboratory Medicinaregatan 9e SE-413 90 Göteborg Sweden ___ 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 Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- Message: 2 Date: Wed, 19 Dec 2007 15:10:41 +0100 From: Jochen Hub [EMAIL PROTECTED] Subject: Re: [gmx-users] HELP REGARDING COMMAND g_pvd To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed avinash kumar wrote: Hello all, I saw a command in the analysis part of manual
[gmx-users] g_hbond (Version 3.3 vs Version 3.14)
Dear All, I found there is some problem with version 3.3 to g_hbond command. Earlier i was using version 3.14, and when i was using g_hbond(v3.14) i found correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so on). But when i use g_hbond (v3.3) then i found it only gives hydrogen bonds between n-n, n-n+1,n-n+2 and rest will have value zero. Is it some bug to version 3.3 or am i doing mistake ! PS:- since i am not sure whether my 1st request has been posted or not, that's why posting again! thanks in advance. Regards, anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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] g_hbond (v 3.14) vs g_hbond (3.3)
Dear Users, I have done clustering of equilibrium ensemble of octa-alanine model system, and when i was trying to find the no. of hydrogen bonds for each cluster, i found different result with different versions. Is there some bug to version 3.3 in comparison of version 3.14 or am i doing the wrong way. Please guide me. I have used the command g_hbond_mpi -f *.pdb -s *.tpr -num hbnum.xvg -hx hbhelix.xvg -r 0.35 -a 30 n-n n-n+1 n-n+2 n-n+3 n-n+4 n-n+5 n-n6 0 0 73 180 277 103618563422Cut-off r=0.35 a=30v3.14 0 0 330 243 358 138221704483Cut-off r=0.35 a=60v3.14 12252373404 0 0 0 0 4002Cut-off r=0.35 a=30v3.3 PS: In version 3.14 the default is r = 0.35 and a = 60 and in version 3.3 the default is r = 0.35 and a = 30 My worry is that when i did calculation with v 3.3 i got more no of n-n n-n+1 and n-n+2 hydrogen bonds, while on the same system with v 3.14 i found 0(Zero) value for n-n n-n+1 and n-n+2 (Quite Surprising with v3.3!) How come hydrogen bond between n-n is possible, when structures and everything is fine. Thanks in advance, With Regards Anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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] g_hbond (method)
Dear all, I would like to know the actual cut-off angle used by gromacs package to calculate Hydrogen bond. since in User manual of version 3.2 and earlier, it was written á equal to or lesser than áHB = 60 degree While in User manual of version 3.3, it is mentioned as á equal to or lesser than áHB = 30 degree so,in actual whether program uses 30 degree or 60 degree in all versions of GROMACS packages. I hope and believe that it (GROMACS) uses 30 degree cut-off criteria for angle (standard and typical value). Thanks in Advance, With Regards, Anil ___ 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: Error while doing EM in DMSO.
Dear David, Thanks for advice, i had made the changes but still getting the same error that Fatal error: Atomtype 'SD' not found! SDMSO 32.06000 ; DMSO Sulphur (solvent) CDMSO 15.03500 ; DMSO Carbon (solvent) ODMSO 15.99940 ; DMSO Oxygen (solvent) **Changes Made in ffG43a1.atp file*** SD 32.06000 ; DMSO Sulphur (solvent) CD 15.03500 ; DMSO Carbon (solvent) OD 15.99940 ; DMSO Oxygen (solvent) I am totally helpless and clueless in finding my mistakes.Any help,hint, suggestions are most welcome. Thanks, With Regards anil Today's Topics: 1. Re: Error while doing EM in DMSO. (David van der Spoel) Date: Wed, 16 May 2007 21:07:54 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Error while doing EM in DMSO. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anil Kumar wrote: Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. If the problem is the missing masses, then just add them in the [atoms] section. (Chapter 5) -- 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] Error while doing EM in DMSO.
Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. ***changes made*** [ DMSO ] [ atoms ] SD SD 0.13900 0 OD OD-0.45900 0 CD1 CD 0.16000 0 CD2 CD 0.16000 0 [ bonds ] SD ODgb_38 SD CD1gb_39 SD CD2gb_39 OD CD1gb_44 OD CD2gb_44 CD1 CD2gb_45 [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type *DMSO before changes** [ DMSO ] [ atoms ] SDmso SDMSO 0.13900 0 ODmso ODMSO-0.45900 0 CDms1 CDMSO 0.16000 0 CDms2 CDMSO 0.16000 0 [ bonds ] SDmso ODmsogb_38 SDmso CDms1gb_39 SDmso CDms2gb_39 ODmso CDms1gb_44 ODmso CDms2gb_44 CDms1 CDms2gb_45 [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type *** dmso.itp file which i am using for dmso is following. [ moleculetype ] ; name nrexcl DMSO2 [ atoms ] ; nrtype resnr residu atomcgnrcharge 1 SD 1 DMSOSD 10.139 2 CD 1 DMSOCD1 10.16 3 OD 1 DMSOOD 1 -0.459 4 CD 1 DMSOCD2 10.16 [ bonds ] ; aiaj funct b0 kb 1 2 1 0.195 376560 ; kb from Methionine 1 3 1 0.153 502080 ; kb from C=O bond 1 4 1 0.195 376560 [ angles ] ; aiajak functtheta kt 3 1 2 1 106.75 460.240 3 1 4 1 106.75 460.240 2 1 4 197.40 460.240 ; kt from Methionine [ dihedrals ] ; ai aj ak al funct xi kxi 1 2 4 3 2 35.264 334.720; default params Any suggestions, hints or helps are most appreciated. Thanks in advance, With Regards anil Message: 1 Date: Sat, 12 May 2007 16:59:40 +0530 (IST) From: Anil Kumar [EMAIL PROTECTED] Subject: [gmx-users] Error while running grompp for em (MD) in Urea To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=iso-8859-1 Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below. I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. Please help me, where does am i making the mistakes. processing coordinates... Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 3 [file base.top, line 808]: 6150 non-matching atom names atom names from base.top will be used atom names from after_sol.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 945 # G96BONDS: 128 # ANGLES: 1215
[gmx-users] Error while running MD in DMSO!
Dear All, I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it is running fine but while running in DMSO. After running genbox i am having problem in running grompp for energy minimization. Error which i got is given below. Cleaning up temporary file gromppkkHvWC Fatal error: Atomtype 'SD' not found! Please, anyone let me know why it is happening when i had used the dmso.gro and dmso.itp files which is available by default to top folder. Thanks in advance. With Warm Regards Anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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] Error while running grompp for em (MD) in Urea
Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below. I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. Please help me, where does am i making the mistakes. processing coordinates... Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 3 [file base.top, line 808]: 6150 non-matching atom names atom names from base.top will be used atom names from after_sol.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 945 # G96BONDS: 128 # ANGLES: 1215 # G96ANGLES: 190 # PDIHS: 1134 # IDIHS: 485 # LJ14: 1242 # SETTLE: 2050 ERROR 4 [file base.top, line 808]: atom C1 (Res UREA-11) has mass 0 ERROR 5 [file base.top, line 808]: atom O2 (Res UREA-11) has mass 0 ERROR 6 [file base.top, line 808]: atom N3 (Res UREA-11) has mass 0 ERROR 7 [file base.top, line 808]: atom H4 (Res UREA-11) has mass 0 ERROR 8 [file base.top, line 808]: atom H5 (Res UREA-11) has mass 0 ERROR 9 [file base.top, line 808]: atom N6 (Res UREA-11) has mass 0 ERROR 10 [file base.top, line 808]: atom H7 (Res UREA-11) has mass 0 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I'm An Oakman (Pulp Fiction) Thanks in advance. With Warm Regards anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: CNT Potassium doping with GROMACS (George Abadir) 2. Re: Cannot find fftw3f (Mark Abraham) 3. Re: suggest small revision to genbox (bharat v. adkar) 4. Re: suggest small revision to genbox (David van der Spoel) 5. Error while running MD in DMSO! (Anil Kumar) -- Message: 1 Date: Fri, 11 May 2007 18:52:43 -0700 From: George Abadir [EMAIL PROTECTED] Subject: Re: [gmx-users] CNT Potassium doping with GROMACS To: [EMAIL PROTECTED],Discussion list for GROMACS users gmx-users
[gmx-users] Problem of memory allocation while doing g_cluster
Hi All, I am in need of kind help from any of gmx user regarding the memory allocatin which i was facing while doing g_cluster. I was trying to do clustering of 33000 strucutres and more of octa-alanine (having 61 lines per pdb). Command i used was: - echo 4 4 | g_cluster_mpi -f total.pdb -s full*.tpr -g clu_total.log -cl clu.pdb -fit -av -method gromos -cutoff 0.15 -ntr -tr totaltrans -clid clust-id.xvg Note:-(Total no. of line in total.pdb = 2013000), Error message: - Last frame 32999 time 167995.016 Allocated 11088000 bytes for frames Read 33000 frames from trajectory 168000.pdb Fatal error: calloc for m[i] (nelem=33000, elsize=4, file matio.c, line 63): Cannot allocate memory What i understood was it is problem in generating array of array (two dimensional array) that's why it crashed Since i have no backgroud of computer science i am not able to fix this problem. Any help !! Thanks in advance Anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) --- Education is a progressive discovery of our ignorance - Will Durant ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
