[gmx-users] how to deal with xleap to simulate a protein-ligand complex?
dear users in order to simulate a Kinase protein attached with two ligands (MG and ATP in particular), i am trying to use amber03 force field with xleap in amber10 (based on some relevant litratures). in fact i am going through a tutorial introduced by Justin Lemkul, entitled protein ligand complex, to learn how to do the simulation. but i dont know how to deal with xleap. is it some thing like PRODGR, mentioned in the tutorial to deal with the ligand? all the best! sajad -- 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] how to deal with xleap to simulate a protein-ligand complex?
On 4/19/2011 6:18 PM, Sajad Ahrari wrote: dear users in order to simulate a Kinase protein attached with two ligands (MG and ATP in particular), i am trying to use amber03 force field with xleap in amber10 (based on some relevant litratures). in fact i am going through a tutorial introduced by Justin Lemkul, entitled protein ligand complex, to learn how to do the simulation. but i dont know how to deal with xleap. is it some thing like PRODGR, mentioned in the tutorial to deal with the ligand? all the best! sajad The LeAP family of tools belongs to the AmberTools package, not GROMACS. Please seek help and documentation there, not here. 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/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] Problem g_x2top
Good morning I was working with x2top version 4.0.7 I put my new atoms in ffoplsaa.n2t file and the program worked without problems I got a reasonable topology of my compound but the program couldn't create a rtp file. Now I have started to work with g_x2top version 4.5.3 and I copied all my new atoms from ffoplsaa.n2t to atomname2type.n2t in /oplsaa.ff directory. When I run g_x2top -f alop.pdb -o alpo.top -ff oplsaa -pbc the program show me the typical error Can not find forcefield for atom O7 with 0 bonds I don't know what happens because in version 4.07 all work OK but in the new version no, can you help me with this problem? Thanks a lot This message was sent using IMP, the Internet Messaging Program. -- 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] binding_affinity
Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -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] binding_affinity
shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -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] binding_affinity
Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -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 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] binding_affinity
shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. -Justin Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -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 -- 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] binding_affinity
Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -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] how to prepare implicit solvent system??
Dear experts, hi, I'm using Gromacs for implicit solvent system, Can anybody let me know hot to prepare the implicit solvent system?? Thanks -- 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] how to prepare implicit solvent system??
김현식 wrote: Dear experts, hi, I'm using Gromacs for implicit solvent system, Can anybody let me know hot to prepare the implicit solvent system?? Just as you would any other system, except you don't need to define a unit cell full of water and ions. pdb2gmx, grompp, mdrun. There are benchmarks and example input files on the Gromacs site. -Justin Thanks -- 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] how to prepare implicit solvent system??
김현식 wrote: If i want to use implicit solvent, genbox step is indispensable ? or Just GBSA in mdp file can effect like solvation ? It sounds like you need to do a bit of literature/textbook reading before you continue. If you're using implicit solvent, then you don't need explicit solvent. That's sort of the point. -Justin Date: Tue, 19 Apr 2011 09:49:25 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] how to prepare implicit solvent system?? 김현식 wrote: Dear experts, hi, I'm using Gromacs for implicit solvent system, Can anybody let me know hot to prepare the implicit solvent system?? Just as you would any other system, except you don't need to define a unit cell full of water and ions. pdb2gmx, grompp, mdrun. There are benchmarks and example input files on the Gromacs site. -Justin Thanks -- 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 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] saving coordinates
Hello Justin, THanks for your reply. Suppose any atom that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. For these atom how gromacs save the coordinate. Does it save the coordinate when it enter from left-hand face? Nilesh On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, If some part of molecule is outside the box. How Gromacs save the coordinates in trajectory. There is no such thing as outside in a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit ions -Justin Nilesh -- 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
Re: [gmx-users] saving coordinates
Nilesh Dhumal wrote: Hello Justin, THanks for your reply. Suppose any atom that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. For these atom how gromacs save the coordinate. Does it save the coordinate when it enter from left-hand face? Presumably. Look in the code, but I suspect this is indeed the case and the reason why trjconv -pbc nojump and other such operations are useful. -Justin Nilesh On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, If some part of molecule is outside the box. How Gromacs save the coordinates in trajectory. There is no such thing as outside in a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit ions -Justin Nilesh -- 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] saving coordinates
Hey :) With domain decomposition the particles are saved with the coordinates corresponding to the position in the rectangular brick with sides equal to the diagonal elements of your unit cell. With particle decomposition the positions are taken for which holds that the first atom of the molecule the particle is part of is in that box. Cheers, Tsjerk On Apr 19, 2011 4:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Nilesh Dhumal wrote: Hello Justin, THanks for your reply. Suppose any atom that leaves... Presumably. Look in the code, but I suspect this is indeed the case and the reason why trjconv -pbc nojump and other such operations are useful. -Justin Nilesh On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: ... -- 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] Studying protein folding: An approach
Dear Community. I am a beginner user of Gromacs for this reason I would like to consult my case. Nowadays, I am studying a protein which folding process has experimental data (especially for a mutant). Structural information about how a mutant destabilizes secondary structure was recently published. The work shown how gradually increasing 1 C degree the structure is affected (from 18 to 20 C). I would like to study the process in silico, but I don´t know what parameters put in the .mdp file. Please their advices or help would be appreciated. Best Regards. Miguel Quiliano -- 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] Re: energy group exclusions
Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try 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/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 -- 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] Re: energy group exclusions
Also, in the case of spc/e bulk water when I do md rerun with SOL SOL exlcusion I see forces on water atoms, however I was expecting it to be zero. On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak symasha...@gmail.comwrote: Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try 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/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 -- 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] Studying protein folding: An approach
Hello Miguel Quiliano, I have been working with Protein Structure Prediction. But, my research is computation area which means to develop an algorithm to try study it. Maybe the paper below helps you. Reproducible Polypeptide Folding and Structure Prediction using Molecular Dynamics Simulations M. Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der Spoel doi:10.1016/j.jmb.2005.09.030 You can find more details about mdp file in http://www.gromacs.org/Documentation/How-tos/Beginners I hope these information help you. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Tue, Apr 19, 2011 at 12:53 PM, Miguel Quiliano Meza rifaxim...@gmail.com wrote: Dear Community. I am a beginner user of Gromacs for this reason I would like to consult my case. Nowadays, I am studying a protein which folding process has experimental data (especially for a mutant). Structural information about how a mutant destabilizes secondary structure was recently published. The work shown how gradually increasing 1 C degree the structure is affected (from 18 to 20 C). I would like to study the process in silico, but I don´t know what parameters put in the .mdp file. Please their advices or help would be appreciated. Best Regards. Miguel Quiliano -- 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
[gmx-users] atomname2type.n2t file for CNT in amber99
Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. Any help is much appreciated. Thanks, Majid -- 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] atomname2type.n2t file for CNT in amber99
majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- 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] DNA molecule builder compatible with gromacs amber ff
Dear gmx-users, this seems like a trivial problem but has driven me crazy: I have been trying to build a simple B-form dsDNA strand for use in MD simulations using Amber99sb. I have tried several platforms and each generates a pdb file which pdb2gmx cannot convert as it cannot understand the naming system of the other platforms. Is there any platform that can be used to create DNA molecules with a naming system compatible with GROMACS, specifically with the Amber99sb ff? Thanks Will -- 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] DNA molecule builder compatible with gromacs amber ff
william Stebbeds wrote: Dear gmx-users, this seems like a trivial problem but has driven me crazy: I have been trying to build a simple B-form dsDNA strand for use in MD simulations using Amber99sb. I have tried several platforms and each generates a pdb file which pdb2gmx cannot convert as it cannot understand the naming system of the other platforms. It would be helpful to know what you've tried, what didn't work, etc. Is this not simply a matter of find-and-replace in a text editor? Is there any platform that can be used to create DNA molecules with a naming system compatible with GROMACS, specifically with the Amber99sb ff? Do Amber's tools not generate compatible input, like NAB and xLeap? -Justin Thanks Will -- 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] Re: energy group exclusions
I just did 2 tests in first I do md rerun with SOL SOL exclusions along with PME option then I get forces on water atoms but in second case when I use Cut-Off for electrostatic forces are zero... not sure why PME introduces forces despite using energy exclusion group... On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak symasha...@gmail.comwrote: Also, in the case of spc/e bulk water when I do md rerun with SOL SOL exlcusion I see forces on water atoms, however I was expecting it to be zero. On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak symasha...@gmail.comwrote: Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try 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/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 -- 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] atomname2type.n2t file for CNT in amber99
Yes, I saved this atomname2type.n2t file in amber99.ff, and my g_x2top command was: g_x2top -f cnt.gro -o cnt.top -ff select, and then I selected amber99 (4th option). Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, April 19, 2011 10:40:53 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- 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
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_239 0 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, April 19, 2011 10:40:53 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- 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
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- 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/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 mailto: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
[gmx-users] comparison of covariance analysis and normal mode analysis for entropy calculations
Dear GMX-Users, I was wondering if anyone compared the entropy estimates obtained from covariance analysis and normal mode analysis for a simple one-well case, using the GROMACS 4.5 version. If so, how well do these match? Best, Hari === Hari S.Muddana Postdoctoral Scholar (Gilson Group) University of California, San Diego -- 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] atomname2type.n2t file for CNT in amber99
Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds. Thanks for your help, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tue, April 19, 2011 11:47:44 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://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/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 mailto: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 -- 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] atomname2type.n2t file for CNT in amber99
majid hasan wrote: Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds. Then it sounds like something in your shell environment is not set properly, either sourcing the wrong GMXRC or setting PATHs or something similar incorrectly. Keep this in mind for the future. -Justin Thanks for your help, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 11:47:44 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- 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 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 mailto:gmx-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/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto: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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Yea, sure, thanks. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tue, April 19, 2011 12:09:06 PM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds. Then it sounds like something in your shell environment is not set properly, either sourcing the wrong GMXRC or setting PATHs or something similar incorrectly. Keep this in mind for the future. -Justin Thanks for your help, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 11:47:44 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://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 mailto:gmx-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/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto: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
[gmx-users] pdb2gmx segmentation fault
Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Please let me know what am I missing. Thanks and Regards, Raghu -- 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] Re: energy group exclusions
On 4/20/2011 4:14 AM, Sikandar Mashayak wrote: I just did 2 tests in first I do md rerun with SOL SOL exclusions along with PME option then I get forces on water atoms but in second case when I use Cut-Off for electrostatic forces are zero... not sure why PME introduces forces despite using energy exclusion group... Because that's how PME works. Part of the electrostatic non-bonded contribution is done in reciprocal space, and that can't be readily decomposed into group-wise contributions. Mark On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com wrote: Also, in the case of spc/e bulk water when I do md rerun with SOL SOL exlcusion I see forces on water atoms, however I was expecting it to be zero. On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com wrote: Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups. What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets of atoms for energy groups and such exclusions are defined by the index groups, not molecules. See manual 7.3 and wherever it talks about groups in an early chapter. On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com wrote: Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even though we have excluded protein-protein interactions? Bonded interactions are unaffected, as you will see if you try it. Mark -- gmx-users mailing list gmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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/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 mailto: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
Re: [gmx-users] pdb2gmx segmentation fault
On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. 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/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] any software which could convert a polypeptide sequence to a pdb file?
Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! - Chuan -- 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] any software which could convert a polypeptide sequence to a pdb file?
Hi, It seems like you look into modelling the polypeptide, if you have a good template you can use pymol ot even insight. If you wish to have an ab-initio model you can use sybyl or alike. Good luck with it, Itamar On 20/04/11 2:36 PM, Liao Chuan wrote: Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! - Chuan -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] any software which could convert a polypeptide sequence to a pdb file?
On 4/20/2011 2:36 PM, Liao Chuan wrote: Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! Leap in the AmberTools package is good for this. 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/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
答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
HI, Itamer and Mark, thanks for your prompt replies. Pymol, Amber and Sybyl are commercial software. Any free software/scripts? - Chuan _ 发件人: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] 代表 Mark Abraham 发送时间: 2011年4月20日 13:31 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? On 4/20/2011 2:36 PM, Liao Chuan wrote: Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I’ve got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! Leap in the AmberTools package is good for this. 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/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: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
On 4/20/2011 3:49 PM, Liao Chuan wrote: HI, Itamer and Mark, thanks for your prompt replies. Pymol, Amber and Sybyl are commercial software. Any free software/scripts? There's a reason I said AmberTools. Google is your friend. Mark - Chuan *发件人:*gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *代表 *Mark Abraham *发送时间:*2011年4月20日 13:31 *收件人:*Discussion list for GROMACS users *主题:*Re: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? On 4/20/2011 2:36 PM, Liao Chuan wrote: Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I’ve got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! Leap in the AmberTools package is good for this. 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/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] Coarse-grained force field
Hello. I am trying to simulate the supramolecular organization of liquid crystalline complex of lanthanide by coarse-grained molecular dynamics. But I have some problems with force fields. I can not find coarse-grained force field for lanthanide ion. Can I use atomistic force field oplsaa.ff for lanthanide ion and Martinin force field for other groups of atoms together in one simulation? Or may be you can recommend me some other coarse-grained force fields? Thank you very much. -- 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: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
Hi Chuan, Leap is a part of Ambertools which is free. See http://ambermd.org/#AmberTools Good luck. Terry 2011/4/20 Liao Chuan liaoch...@tju.edu.cn HI, Itamer and Mark, thanks for your prompt replies. Pymol, Amber and Sybyl are commercial software. Any free software/scripts? - Chuan -- *发件人:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *代表 *Mark Abraham *发送时间:* 2011年4月20日 13:31 *收件人:* Discussion list for GROMACS users *主题:* Re: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? On 4/20/2011 2:36 PM, Liao Chuan wrote: Dear gmx-users, I want to conduct simulations of a protein and its ligand, a heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. Thus, I will have to conduct a total number of 4*4*4=64 runs. I’ve got the pdb file of the protein, but I have no idea how to prepare the pdb files of those 64 heptapeptides with sequences already known. Is there any software/script which could convert a polypeptide sequence to a pdb file? Any comment is appreciated! Leap in the AmberTools package is good for this. 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/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
