[gmx-users] Joining two peptide chains
Hi ALL, Is there any way in GROMACS to join two peptide chains by forming a peptide bond between the C and N atoms? Any suggestion is welcome. Regards, Anirban -- 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] g_sas = micelle ?
HI how to calculate SASA of micelle using g_sas? i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the atom numbers of micelle. if micelle is not compact enough but there are no water molecules inside the micelle, will g_sas calculate the vacancy part inside the micelle? Or, if there exists water molecules inside the micelle, will g_sas calculate the water/micelle interface part inside the micelle? Thank you Lin -- 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] Random Accelerator Molecular Dynamics
Hi all I would like to know whether Random Accelerator Molecular Dynamics is available in Gromacs as it is available in AMBER. E R Azhagiya singam -- 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] g_sas = protein and ligand aggregate interface area ?
HI As David said, = How to compute protein-protein interface area? If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB I want to calculate protein and ligand aggregate (small micelle of ligand) interface area. Is it the same step as calculation of protein A and B interface, which David mentioned above? But replacing protein B to Ligand aggregate (small micelle of ligand) ? g_sas -n ligand-micelle-index.ndx ? where ligand-micelle-index.ndx includes all the atom numbers of ligand micelle, which attached on the protein . Is my idea correct? Thank you Lin -- 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] Joining two peptide chains
Hi ALL, Is there any way in GROMACS to join two peptide chains by forming a peptide bond between the C and N atoms? Any suggestion is welcome. Regards, Anirban -- 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
Re: [gmx-users] g_sas = protein and ligand aggregate interface area ?
Hey Lin, Is it the same step as calculation of protein A and B interface, which David mentioned above? But replacing protein B to Ligand aggregate (small micelle of ligand) ? g_sas -n ligand-micelle-index.ndx ? Of course. Is my idea correct? Is it necessary to always question your ability to think in public? You could try and draw your problem, and you could try to see if things turn out the way you expect them under the assumption that your thoughts were correct. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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
Re: [gmx-users] Joining two peptide chains
Hi Anirban, If you have the two chains in one file, with identical chain identifiers and no TER statement in case it's a PDB file, then running pdb2gmx will actually create the bond between them (no matter how far away the termini are). Cheers, Tsjerk On Fri, Apr 9, 2010 at 9:37 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, Is there any way in GROMACS to join two peptide chains by forming a peptide bond between the C and N atoms? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] Re: converting parmbsc0 dihedrals to RB function
Hi Guillem, Many thanks for your clarification. I was lazy to find out and remember why psc0 was not ported to GMX by ffAmber previously and it was exactly because what you've said. And because I was not confident enough, I didn't implement that for acpypi, which I believe does better than amb2gmx in general, so I would be glad if you could take a look at it and if you could let me know which modifications you did to amb2gmx. I am taking plunge in this problem again and I'll try to come out with a solution based in what you suggest. Cheers, Alan On Fri, Apr 9, 2010 at 00:53, gmx-users-requ...@gromacs.org wrote: Right, the only dihedral angles that do not allow an exact translation to RB because of the phase are the ones involving the new parametrization for nucleic acids. Namely, it corrects the alpha/gamma transitions to get the populations of states right, thus avoiding the loss of helicity on the long run. For proteins, there's no difference at all, so you can use ffamber. I've used the combined approach you mention without problems. The only thing is that I do not use pdb2gmx. Rather I use amber's tools (leap+libraries, all free in ambertools) to get a topology, and then I use a slightly modified version of amb2gmx.pl script to get a gromacs topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase does not allow a direct conversion to RB form. Typically you have three entries for the same dihedral, this is no problem at the itp level, grompp captures them all. With this approach I reproduced a torsional scan of parmbsc0 from amber md tool using gromacs, so I feel confident about it. Another option is to use the ffamber parameters and change the itp file including the new ones. I should also mention that I had problems importing the new dihedrals using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if type 1 or 3 is used. There was a new dihedral type that could be used in the development versions, but... for a reason it did not work out for me, don't recall exactly why. It could well be that it would have worked with more patience from my side. Hope this helped, somehow. You were on the right direction anyway. best, Guillem -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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] Re: converting parmbsc0 dihedrals to RB function
Hi Alan, I have no experience with acpypi, so I can't tell which one does better, or why... rdparm not being needed, that would be a strong point. Unfortunately, I'm running a bit short of time at the moment, so I can't really spend a lot of time looking into unknown codes, hope you understand... Nevertheless, the modifications are straightforward : if the phase of the dihedral in question is different than 0 or 180, then you should print the 3 dihedrals as type 1 - and converting the units -, instead of combining them as RB. I did not do anything else to amb2gmx. best of luck, Guillem Alan wrote: Hi Guillem, Many thanks for your clarification. I was lazy to find out and remember why psc0 was not ported to GMX by ffAmber previously and it was exactly because what you've said. And because I was not confident enough, I didn't implement that for acpypi, which I believe does better than amb2gmx in general, so I would be glad if you could take a look at it and if you could let me know which modifications you did to amb2gmx. I am taking plunge in this problem again and I'll try to come out with a solution based in what you suggest. Cheers, Alan On Fri, Apr 9, 2010 at 00:53, gmx-users-requ...@gromacs.org wrote: Right, the only dihedral angles that do not allow an exact translation to RB because of the phase are the ones involving the new parametrization for nucleic acids. Namely, it corrects the alpha/gamma transitions to get the populations of states right, thus avoiding the loss of helicity on the long run. For proteins, there's no difference at all, so you can use ffamber. I've used the combined approach you mention without problems. The only thing is that I do not use pdb2gmx. Rather I use amber's tools (leap+libraries, all free in ambertools) to get a topology, and then I use a slightly modified version of amb2gmx.pl script to get a gromacs topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase does not allow a direct conversion to RB form. Typically you have three entries for the same dihedral, this is no problem at the itp level, grompp captures them all. With this approach I reproduced a torsional scan of parmbsc0 from amber md tool using gromacs, so I feel confident about it. Another option is to use the ffamber parameters and change the itp file including the new ones. I should also mention that I had problems importing the new dihedrals using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if type 1 or 3 is used. There was a new dihedral type that could be used in the development versions, but... for a reason it did not work out for me, don't recall exactly why. It could well be that it would have worked with more patience from my side. Hope this helped, somehow. You were on the right direction anyway. best, Guillem -- 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] Re: converting parmbsc0 dihedrals to RB function
Hi Guillem! Thanks! and sorry, you don't need to look the code, just use it when trying amb2gmx and case you noticed something suspect I would be glad to be informed. So no need to waste your time other than when *really* needing to use amb2gmx. Your solution is what I have in mind and what I am doing to test. Thanks again, Alan On Fri, Apr 9, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: Hi Alan, I have no experience with acpypi, so I can't tell which one does better, or why... rdparm not being needed, that would be a strong point. Unfortunately, I'm running a bit short of time at the moment, so I can't really spend a lot of time looking into unknown codes, hope you understand... Nevertheless, the modifications are straightforward : if the phase of the dihedral in question is different than 0 or 180, then you should print the 3 dihedrals as type 1 - and converting the units -, instead of combining them as RB. I did not do anything else to amb2gmx. best of luck, Guillem -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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] mdsimulation of drug enzyme complex
Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Abhijit -- 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
Re: [gmx-users] mdsimulation of drug enzyme complex
abhijit kayal wrote: Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Have you looked into the list archive? This blowing up error has been reported, diagnosed, and solved hundreds (if not thousands) of times, and there are only a few reasons why it's happening. Also: http://www.gromacs.org/Documentation/Terminology/Blowing_Up From your description, it sounds as if the topology is constructed incorrectly, since your two separate ligands are being considered one molecule and thus experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of times), face-value PRODRG topologies are often unsatisfactory (and thus unreliable) without modification of charges and charge groups. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Abhijit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] mdsimulation of drug enzyme complex
Hi Thank you for your quick reply. As you mentioned I went through the mailing list search. And I am thinking my error occured at the system preparation with taking the two ligands. Earlier I ran md simulation taking the ligand individually and it was showing no error. So the topolgy I got from the PRODRG server is fine. So input file may be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand. On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: abhijit kayal wrote: Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Have you looked into the list archive? This blowing up error has been reported, diagnosed, and solved hundreds (if not thousands) of times, and there are only a few reasons why it's happening. Also: http://www.gromacs.org/Documentation/Terminology/Blowing_Up From your description, it sounds as if the topology is constructed incorrectly, since your two separate ligands are being considered one molecule and thus experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of times), face-value PRODRG topologies are often unsatisfactory (and thus unreliable) without modification of charges and charge groups. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Abhijit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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
Re: [gmx-users] mdsimulation of drug enzyme complex
abhijit kayal wrote: Hi Thank you for your quick reply. As you mentioned I went through the mailing list search. And I am thinking my error occured at the system preparation with taking the two ligands. Earlier I ran md simulation taking the ligand individually and it was showing no error. So the topolgy I got from the PRODRG server is fine. So input file may Be prepared to justify that the topology is fine to a reviewer. Every time I have generated a PRODRG topology, some aspect of its atom types, charges, or charge groups has been wrong. You always need to prove your parameters are valid (hence the link I posted) or else you are wasting a lot of time doing meaningless MD with a flawed physical model. be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand. I have no idea. Are your ligands different? The same? If they're the same, then there is absolutely no reason why you can't simply: #include ligand.itp [ molecules ] LIG 2 Without seeing your topology or getting a better sense of what it is you did, there's not much more to offer. GROMACS isn't magically converting one molecule into two; somehow the instructions you're providing grompp and/or mdrun are causing the problem. -Justin On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: abhijit kayal wrote: Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Have you looked into the list archive? This blowing up error has been reported, diagnosed, and solved hundreds (if not thousands) of times, and there are only a few reasons why it's happening. Also: http://www.gromacs.org/Documentation/Terminology/Blowing_Up From your description, it sounds as if the topology is constructed incorrectly, since your two separate ligands are being considered one molecule and thus experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of times), face-value PRODRG topologies are often unsatisfactory (and thus unreliable) without modification of charges and charge groups. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Abhijit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list
Re: [gmx-users] mdsimulation of drug enzyme complex
Hi Justin, No my ligand is different. And my topolgy look like this #include ffG43a1.itp #include rrg.itp #include drg.itp and at the end it is like this Protein 1 RRG 1 DRG 1 SOL 17662 But I cannot understand where my topology is wrong. What I did is that I docked a ligand at active site then another ligand at the active site. Then I separate the ligands coordinate and generate .gro,.itp file using PRODRG server. Please reply Abhijit On Fri, Apr 9, 2010 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu wrote: abhijit kayal wrote: Hi Thank you for your quick reply. As you mentioned I went through the mailing list search. And I am thinking my error occured at the system preparation with taking the two ligands. Earlier I ran md simulation taking the ligand individually and it was showing no error. So the topolgy I got from the PRODRG server is fine. So input file may Be prepared to justify that the topology is fine to a reviewer. Every time I have generated a PRODRG topology, some aspect of its atom types, charges, or charge groups has been wrong. You always need to prove your parameters are valid (hence the link I posted) or else you are wasting a lot of time doing meaningless MD with a flawed physical model. be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand. I have no idea. Are your ligands different? The same? If they're the same, then there is absolutely no reason why you can't simply: #include ligand.itp [ molecules ] LIG 2 Without seeing your topology or getting a better sense of what it is you did, there's not much more to offer. GROMACS isn't magically converting one molecule into two; somehow the instructions you're providing grompp and/or mdrun are causing the problem. -Justin On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: abhijit kayal wrote: Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Have you looked into the list archive? This blowing up error has been reported, diagnosed, and solved hundreds (if not thousands) of times, and there are only a few reasons why it's happening. Also: http://www.gromacs.org/Documentation/Terminology/Blowing_Up From your description, it sounds as if the topology is constructed incorrectly, since your two separate ligands are being considered one molecule and thus experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of times), face-value PRODRG topologies are often unsatisfactory (and thus unreliable) without modification of charges and charge groups. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Abhijit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search
Re: [gmx-users] mdsimulation of drug enzyme complex
abhijit kayal wrote: Hi Justin, No my ligand is different. And my topolgy look like this #include ffG43a1.itp #include rrg.itp #include drg.itp and at the end it is like this Protein 1 RRG 1 DRG 1 SOL 17662 But I cannot understand where my topology is wrong. What I did is that I docked a ligand at active site then another ligand at the active site. Then I separate the ligands coordinate and generate .gro,.itp file using PRODRG server. Please reply Since you have two different ligands, you will inherently have two [moleculetype] definitions, between which no bonded interactions can be specified. You should take another look at the atoms mdrun is complaining about; I see no possible way that they can belong to atoms of different molecules. To ultimately solve the problem, refer to the blowing up link I provided before. Something about your model physics (parameters, .mdp settings, etc) is unrealistic. -Justin Abhijit On Fri, Apr 9, 2010 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: abhijit kayal wrote: Hi Thank you for your quick reply. As you mentioned I went through the mailing list search. And I am thinking my error occured at the system preparation with taking the two ligands. Earlier I ran md simulation taking the ligand individually and it was showing no error. So the topolgy I got from the PRODRG server is fine. So input file may Be prepared to justify that the topology is fine to a reviewer. Every time I have generated a PRODRG topology, some aspect of its atom types, charges, or charge groups has been wrong. You always need to prove your parameters are valid (hence the link I posted) or else you are wasting a lot of time doing meaningless MD with a flawed physical model. be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand. I have no idea. Are your ligands different? The same? If they're the same, then there is absolutely no reason why you can't simply: #include ligand.itp [ molecules ] LIG 2 Without seeing your topology or getting a better sense of what it is you did, there's not much more to offer. GROMACS isn't magically converting one molecule into two; somehow the instructions you're providing grompp and/or mdrun are causing the problem. -Justin On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: abhijit kayal wrote: Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error 1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size. When I look the particular atoms they corrospond to the last atom of the ligand at the active site and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file. Please help me to find out the problem. Have you looked into the list archive? This blowing up error has
Re: [gmx-users] problem with total energy
Dear Mark and Justin, Thanks for your help, as a beginner to GROMACS i think i have to spend even more time with each option and make sure i know what i am doing. I will spend some time by using different electrostatic options with out pbc and let you know what happens to the simulations. Thanks Srinivas. On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2010 1:25 PM, jampani srinivas wrote: Dear Justin, I am sorry for the poor description of the problem, OK let me explain you clearly here. I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain radius (in this case it is 2.5 nm). To achieve this i made two temperature coupling groups, first (Tmp1) one has protein and waters within 2.5nm from the center of the box and rest is second temperature coupling group (Tmp2). Initially when i run the simulation it was creating nrdf = 0 for both groups, Berk has helped me with a file readir.c file, i compiled my gromacs again that problem was solved. I have submitted simulations again and found that the energy was blowing up. I think you know the story after this. Earlier I want protein to interact with inner wall of the frozen group and check what happens, because of this I have never looked at the energygrps_excl option. I have done with both 2 and 4 fs time steps and I took 4fs option to speed up the simulation, and I have to still look at the paper you suggested me. Thanks for your suggestions, I have implemented your suggestion one after the other, finally when i use the energygrps_excl option it worked out. Now there is no sudden drift in the energy, and also i checked the velocities of non-frozen group is mostly zero (except for first frame) When I use the energygrps_excel option in the following way i am getting the below mentioned note i have to still understand what is this message. On the other hand if i use only energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 line in mdp file i am getting fatal error. Is it necessary to to define the energy groups first and later exclude the energy option? Yes, energy group exclusions require matching energy group definitions. The relevant part of manual 7.3 probably says this. + energygrps = Tmp1 Tmp2 energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 NOTE Can not exclude the lattice Coulomb energy between energy groups You seem to be trying to simulate a droplet inside a rigid shell of water. If so, why do you want the system to be periodic? You don't want periodicity artefacts *and* frozen-water-shell artefacts. There are other electrostatics models better suited than PME to such situations. You should look in the literature for successful published methodologies, rather than risk inventing a square wheel yourself before you've got enough experience to be confident with what you're doing. Here, the reciprocal-space part of the PME calculation must contain contributions from your excluded energy-groups, so you've got some Frankenstein possible worst-of-all-worlds combination. If I got such a paper to review, I'd need to see some serious groundwork justifying such a choice. I used -maxwarn option here and generated the tpr file. I hope this does not harm the simulation. That's a risky strategy. The programmer didn't put in such a message just to see whether he could do it... Mark -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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
Re: [gmx-users] InflateGRO and pentamer protein simulation
xi zhao wrote: I would like to run a simulation of a pentamers in a POPC membrane, and using new inflategro with doughnut mode, but I have met similar result as the links http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also got a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box. Please give me some suggestions! Thank you in advance! best regards! I think the problem comes from pattern matching in the script. With large bilayers, the atom names and numbers will not be split correctly; this could be causing a problem for you. I'd again suggest that you contact the developer of the program and discuss this issue, as it is not really a Gromacs problem and only a few people on this list really use such programs. I think you'll find a resolution faster that way. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年4月9日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful help, you'll have to do a whole lot better than simply saying the results were wrong. No one on this list will have any idea what you mean. If you believe there is some error in the script itself, you're better off contacting its author. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Calculating Area per lipid... Protein X-min/max: 23105 Protein Y-min/max: 18100 X-range: 82 AY-range: 82 A Building 82 X 82 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 49 nm^2
[gmx-users] two reference groups in pull code
Dear all: Reading about the gromacs4 manual, I couldn't figure out a way to apply two sets of pulling simultaneously in gromacs? I know you can specify a second group using pull_group2, but it has to use the same reference group in pull_group0, correct? Then I don't understand how one can achieve to pull a b apart, and also c d apart at the same time. Any suggestion will be greatly appreciated. Thanks, Bin -- 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] CHARMM to GROMACS perl scripts
Hi, Can anybody direct me to where I can find the most recent and updated version of Mark Abraham's perl scripts for converting CHARMM parameters to GROMACS? Many Thanks, Peter -- 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] two reference groups in pull code
Dear Bin: What you request is not currently possible with any distribution up to gmx-4.0.7 (I don't know if it is in the cvs). I have a modified version of gromacs-4.0.5 that will do this, but we are not distributing it yet. We may upload it in the future for incorporation into the main distribution, but currently I'm not sure how to do that. The changes to the gmx-3 source code were not very difficult to get this feature, but the changes to gmx-4 were substantial. If you are ok to use gmx-3 then you should be able to make the mod yourself in a few hours. Chris. -- original message -- Dear all: Reading about the gromacs4 manual, I couldn't figure out a way to apply two sets of pulling simultaneously in gromacs? I know you can specify a second group using pull_group2, but it has to use the same reference group in pull_group0, correct? Then I don't understand how one can achieve to pull a b apart, and also c d apart at the same time. Any suggestion will be greatly appreciated. Thanks, Bin -- 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
Re: [gmx-users] two reference groups in pull code
Dear Chris: Thanks very much for the info. I will take a look at the source code and see how far I can go.;-) Bin On Apr 9, 2010, at 11:38 AM, chris.ne...@utoronto.ca wrote: Dear Bin: What you request is not currently possible with any distribution up to gmx-4.0.7 (I don't know if it is in the cvs). I have a modified version of gromacs-4.0.5 that will do this, but we are not distributing it yet. We may upload it in the future for incorporation into the main distribution, but currently I'm not sure how to do that. The changes to the gmx-3 source code were not very difficult to get this feature, but the changes to gmx-4 were substantial. If you are ok to use gmx-3 then you should be able to make the mod yourself in a few hours. Chris. -- original message -- Dear all: Reading about the gromacs4 manual, I couldn't figure out a way to apply two sets of pulling simultaneously in gromacs? I know you can specify a second group using pull_group2, but it has to use the same reference group in pull_group0, correct? Then I don't understand how one can achieve to pull a b apart, and also c d apart at the same time. Any suggestion will be greatly appreciated. Thanks, Bin -- 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 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] remove from mailing list
Hi All, I send you an email that now I want to remove/delete that but I do't now.my question is how can I remove my email? Thank you _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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
Re: [gmx-users] remove from mailing list
Per the footer of the email: Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -Justin you zou wrote: Hi All, I send you an email that now I want to remove/delete that but I do't now. my question is how can I remove my email? Thank you Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Fe+2 not found in forcefield ffG43a1
Dear Users. Maybe this question is easy for all, but i have problems, patience please. I do not have experience with metals, now I have a protein (crystal) with Fe+2, which is coordinating with three HISTIDINES, one D and two molecules of water, when I try to run pdb2gmx the program tells me Residue FE not found in residue topology database. I opened the database for forcefield ffG43a1 and only found FE for heme group. I search other forcefields for iron+2, but most refer to heme groups. Why? and what happend with Fe+2? What can i do? I would very grateful if someone gives advices or ideas. thanks in advance Miguel -- 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] hou to Construct the oil/water interface
nbsp;nbsp;nbsp;nbsp; nbsp;Hello, I want to construct the oil/water interface, like this:nbsp;X andnbsp;Y axises of the box are 5 nm, Z axis is 10 nm. 0-5 nm ofnbsp;Z axis in the nbsp;box is water, and 5-10 nm ofnbsp;Z axis in the box is oil (for example :dodecane), how can I achieve the aim? nbsp;nbsp;nbsp;nbsp;nbsp; Thank you very much! nbsp;nbsp;nbsp;nbsp;nbsp; nbsp;nbsp;nbsp;nbsp;nbsp; -- 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] g_sas -pbc ???
Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom... ) or, trjconv -center . I could not get what i wanted. Thank you Lin -- 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
Re: [gmx-users] CHARMM to GROMACS perl scripts
Hi, are you aware of the Pär's CHARMM version in the GIT version? Unless you want to do something very special - you probably want to use that over Mark's version. Roland On Fri, Apr 9, 2010 at 2:27 PM, Peter Huwe pjh...@gmail.com wrote: Hi, Can anybody direct me to where I can find the most recent and updated version of Mark Abraham's perl scripts for converting CHARMM parameters to GROMACS? Many Thanks, Peter -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
