Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 3 2 4 1 2 4 5 1 115.95 105.00 So there are lines missing. In my ffbonded.itp angles are all defined like [ angletypes ] ; i j k func th0 cth ub0 cub ; f5: Urey-Bradley NN3A CN1A ON1 5 123.75 250.00 NN3A CN1A NN2U 5 117.47 230.00 CN1A NN2U HN2 5 115.95 105.00 And in my .rtp file it looks like ; Col 1: angle classification ; Col 2: equilibrium bond angles in degrees ; COl 3: force constant in kcal/(mol*rad^2) [ angles ] N1 C2 O2 123.75 250.00 N1 C2 N3 117.47 230.00 C2 N3 H3 115.95 105.00 What is the problem? Why are there still this missing lines in the topology? Thanks for helping me Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:59 Montag, 7.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/7/12 2:54 PM, Lara Bunte wrote: Hi So you think that I should edit something in ffbonded.itp? The parameters that I would write by hand in the topology should be supplemented in the ffbonded.itp? I don't really know what I have to do concretely, to fix this problem. If the parameters are not already present in the force field, you have 2 options: 1. Add them to ffbonded.itp - useful if you have multiple molecules that you need to simulate 2. Add them to the topology - the easiest approach Both effectively accomplish the same thing, but approach #2 is slightly more straightforward and does not potentially affect all your simulations should something go wrong. -Justin Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors: ERROR 28 [file topol.top, line 229]: No default Angle types ERROR 29 [file topol.top, line 233]: No default Improper Dih. types My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess). What could be the problem? I am able to complete the topol.top file by hand, but I really like to know what is the problem here. A sequence of atoms in a topology (defined by atom type, not name or number) is mapped back to parameters in ffbonded.itp. If no suitable parameters are found, you get the error messages. In a normal topology (.top or .itp) for most force fields, the parameters are not explicitly stated because they are looked up in this manner. If you're introducing something new or overriding existing force field parameters, you need to explicitly include them in the topology or add them to the appropriate directive in ffbonded.itp. -Justin Thanks for help Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 5/14/12 5:15 PM, Lara Bunte wrote: Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like [ angles ] ; aiajak functc0c1c2c3 2 119 1 1 2 3 1123.75 250.00 1 2 4 1117.47 230.00 3 2 4 1 2 4 5 1115.95 105.00 Well what are these atoms that have missing parameters? By default, pdb2gmx will generate all possible angles based on bonded connectivity. Normally, CHARMM27 topologies have type 5 angles (Urey-Bradley) and the parameters are not explicitly listed. They are looked up from ffbonded.itp when running grompp. So there are lines missing. In my ffbonded.itp angles are all defined like [ angletypes ] ; i j k functh0 cth ub0 cub ; f5: Urey-Bradley NN3ACN1AON1 5 123.75 250.00 NN3ACN1ANN2U 5 117.47 230.00 CN1ANN2UHN2 5 115.95 105.00 The mismatch here between function type in ffbonded.itp (5) and that which is present in the topology (1) suggests something is more fundamentally wrong here. And in my .rtp file it looks like ; Col 1: angle classification ; Col 2: equilibrium bond angles in degrees ; COl 3: force constant in kcal/(mol*rad^2) [ angles ] N1C2O2 123.75 250.00 N1C2N3 117.47 230.00 C2N3H3 115.95 105.00 What is the problem? Why are there still this missing lines in the topology? Perhaps you haven't considered all possible angles. Perhaps there's something more systemically incorrect in what you've set up. Based on a few snippets of topology and force field files, unfortunately it's impossible to say at this point. -Justin -- Justin A. Lemkul, Ph.D. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Hi So you think that I should edit something in ffbonded.itp? The parameters that I would write by hand in the topology should be supplemented in the ffbonded.itp? I don't really know what I have to do concretely, to fix this problem. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors: ERROR 28 [file topol.top, line 229]: No default Angle types ERROR 29 [file topol.top, line 233]: No default Improper Dih. types My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess). What could be the problem? I am able to complete the topol.top file by hand, but I really like to know what is the problem here. A sequence of atoms in a topology (defined by atom type, not name or number) is mapped back to parameters in ffbonded.itp. If no suitable parameters are found, you get the error messages. In a normal topology (.top or .itp) for most force fields, the parameters are not explicitly stated because they are looked up in this manner. If you're introducing something new or overriding existing force field parameters, you need to explicitly include them in the topology or add them to the appropriate directive in ffbonded.itp. -Justin Thanks for help Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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] Missing Interactions in [ angles ] Section in Topology
On 5/7/12 2:54 PM, Lara Bunte wrote: Hi So you think that I should edit something in ffbonded.itp? The parameters that I would write by hand in the topology should be supplemented in the ffbonded.itp? I don't really know what I have to do concretely, to fix this problem. If the parameters are not already present in the force field, you have 2 options: 1. Add them to ffbonded.itp - useful if you have multiple molecules that you need to simulate 2. Add them to the topology - the easiest approach Both effectively accomplish the same thing, but approach #2 is slightly more straightforward and does not potentially affect all your simulations should something go wrong. -Justin Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors: ERROR 28 [file topol.top, line 229]: No default Angle types ERROR 29 [file topol.top, line 233]: No default Improper Dih. types My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess). What could be the problem? I am able to complete the topol.top file by hand, but I really like to know what is the problem here. A sequence of atoms in a topology (defined by atom type, not name or number) is mapped back to parameters in ffbonded.itp. If no suitable parameters are found, you get the error messages. In a normal topology (.top or .itp) for most force fields, the parameters are not explicitly stated because they are looked up in this manner. If you're introducing something new or overriding existing force field parameters, you need to explicitly include them in the topology or add them to the appropriate directive in ffbonded.itp. -Justin Thanks for help Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors: ERROR 28 [file topol.top, line 229]: No default Angle types ERROR 29 [file topol.top, line 233]: No default Improper Dih. types My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess). What could be the problem? I am able to complete the topol.top file by hand, but I really like to know what is the problem here. Thanks for help Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 5/6/12 3:45 PM, Lara Bunte wrote: Hi You said: The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors: ERROR 28 [file topol.top, line 229]: No default Angle types ERROR 29 [file topol.top, line 233]: No default Improper Dih. types My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess). What could be the problem? I am able to complete the topol.top file by hand, but I really like to know what is the problem here. A sequence of atoms in a topology (defined by atom type, not name or number) is mapped back to parameters in ffbonded.itp. If no suitable parameters are found, you get the error messages. In a normal topology (.top or .itp) for most force fields, the parameters are not explicitly stated because they are looked up in this manner. If you're introducing something new or overriding existing force field parameters, you need to explicitly include them in the topology or add them to the appropriate directive in ffbonded.itp. -Justin Thanks for help Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Hi Thanks for the answer. For me I don't know where the problem is. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. I put my .rtp file in the appendix. Could you please take a look on it? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:04 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Peter C. Lai wrote: [ angles ] is defined in ffbonded.itp. If you have new angles you will need to specify them there. grompp will read ffbonded.itp and try to correlate To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles). An [angletypes] directive in ffbonded.itp supplies the parameters for angles. it with the atomnumbers in the top file generated by pdb2gmx. If you modified your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least that is my experience). Correct, but it is still not clear to me what the problem is here, if there is one. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. -Justin On 2012-03-07 05:19:19PM +, Lara Bunte wrote: Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote: Hi Thanks for the answer. For me I don't know where the problem is. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. I put my .rtp file in the appendix. Could you please take a look on it? What's happening here is that the angles explicitly listed in the .rtp file are shown in your .top, but there are other angles present for which you have not specified parameters. These are the lines that have no explicit equilibrium angle and force constant. They will be looked up in ffbonded.itp. -Justin Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:04 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Peter C. Lai wrote: [ angles ] is defined in ffbonded.itp. If you have new angles you will need to specify them there. grompp will read ffbonded.itp and try to correlate To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles). An [angletypes] directive in ffbonded.itp supplies the parameters for angles. it with the atomnumbers in the top file generated by pdb2gmx. If you modified your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least that is my experience). Correct, but it is still not clear to me what the problem is here, if there is one. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. -Justin On 2012-03-07 05:19:19PM +, Lara Bunte wrote: Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
[ angles ] is defined in ffbonded.itp. If you have new angles you will need to specify them there. grompp will read ffbonded.itp and try to correlate it with the atomnumbers in the top file generated by pdb2gmx. If you modified your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least that is my experience). On 2012-03-07 05:19:19PM +, Lara Bunte wrote: Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 1 2 4 1 117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Peter C. Lai wrote: [ angles ] is defined in ffbonded.itp. If you have new angles you will need to specify them there. grompp will read ffbonded.itp and try to correlate To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles). An [angletypes] directive in ffbonded.itp supplies the parameters for angles. it with the atomnumbers in the top file generated by pdb2gmx. If you modified your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least that is my experience). Correct, but it is still not clear to me what the problem is here, if there is one. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. -Justin On 2012-03-07 05:19:19PM +, Lara Bunte wrote: Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 2012-03-07 03:04:28PM -0500, Justin A. Lemkul wrote: Peter C. Lai wrote: [ angles ] is defined in ffbonded.itp. If you have new angles you will need to specify them there. grompp will read ffbonded.itp and try to correlate To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles). An [angletypes] directive in ffbonded.itp supplies the parameters for angles. Yeah. I don't have any [angles] sections in my charmm rtps because I rely on pdb2gmx to generate them from the [bonds] in the .rtp and the [angletypes] from ffbonded.itp it with the atomnumbers in the top file generated by pdb2gmx. If you modified your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least that is my experience). Correct, but it is still not clear to me what the problem is here, if there is one. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. Yeah I was trying to make a guess as to the cause of the OP's problem. To me, the safest way to parameterize a new residue is to focus on putting in the correct additions to ffbonded.itp and ffnonbonded.itp to guarantee that reruns of pdb2gmx will generate the correct topology instead of trying to fix an existing .top. For CHARMM at least, I believe the .rtp entry for the new residue should only have [atoms] [bonds] and [impropers]. -Justin On 2012-03-07 05:19:19PM +, Lara Bunte wrote: Hi Justin I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2 c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2 c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote: Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand to topology but what could be the reason for this problem? What exactly is missing? By default, pdb2gmx generates all possible angles. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 23 1123.75 250.00 1 24 1117.47 230.00 And my pdb2gmx output is for example something like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00 1 2 3 1 1 2 4 1117.47 230.00 So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology? What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so missing parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes. In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
