[gmx-users] retraining multiple protein ligand interactions using pull-code
Hello everyone, I am new to using gromacs. I am currently studying an enzyme catalysing a transfer reaction. there are two substrates and I want to restraint specific interactions between different parts of the ligands and the protein. As I understand so far from reading various discussions in the group, restraining such interactions is possible through pull code, But we can assign only one pull group0, I am wondering if there is better way to restraint multiple interactions between multiple molecules in a single simulation. If not through pull-code, what will be the best way to ensure many specific intermolecular restraints? thank you very much in advance. regards, Saravanan -- 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] retraining multiple protein ligand interactions using pull-code
Thank you.. I hoped it would be simpler. how do I go about creating unified protein-ligand [moleculartype] directives. Can you suggest any material available on this topic? that would be extremely helpful. -Saravanan On 28 March 2013 16:45, Justin Lemkul jalem...@vt.edu wrote: On 3/28/13 4:01 AM, Saravanan wrote: Hello everyone, I am new to using gromacs. I am currently studying an enzyme catalysing a transfer reaction. there are two substrates and I want to restraint specific interactions between different parts of the ligands and the protein. As I understand so far from reading various discussions in the group, restraining such interactions is possible through pull code, But we can assign only one pull group0, I am wondering if there is better way to restraint multiple interactions between multiple molecules in a single simulation. If not through pull-code, what will be the best way to ensure many specific intermolecular restraints? Use distance restraints. Unfortunately, this will require a lot of topology hacking to create unified protein-ligand [moleculetype] directives. Restraints (like any bonded interaction) can only be applied within a [moleculetype], not between them. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Problem with Inflategro!!!
Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Problem with Inflategro!!!
no, water problem is solved, but my protein is still out of the bilayer, When i change:minimize my box vector values and inflate...the protein is packed inside. but now the area per lipid is too low for popc its like 0.148 nm2 On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * 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 -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Problem with Inflategro!!!
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC 14 system_inflated.gro 5 area.dat my gro file looks like, membrane protein in POPC 121-310KWITNOIONS 59522 1SER N1 -2.092 -1.832 -1.359 1SERHT12 -2.149 -1.861 -1.436 1SERHT23 -2.150 -1.809 -1.281 1SER CA4 -2.002 -1.942 -1.322 ... 91ILEOT1 1527 0.033 1.945 -1.049 91ILEOT2 1528 0.057 1.922 -1.267 continued by popc and sol 1POPC N1 2.963 -2.658 2.064 1POPC C122 3.003 -2.713 2.196 1POPC C133 2.954 -2.509 2.062 . 8764SOL OW57992 3.731 3.721 -2.405 8764SOLHW157993 3.749 3.653 -2.341 8764SOLHW257994 3.723 3.802 -2.353 11.13710 11.41790 7.60370 when I inflate with box vectors value 11.13710 11.41790 7.60370, my protein is out of inflated lipid boundary. if i change my value to 1.39213 1.42723 0.0 (dividing above value by half and half), now my protein is at the center of inflated popc. but the area per lipid even after inflation is still only 0.148 nm2. should i use editconf with the whole .gro file containing protein, popc or i have to separate my protein only as a new.gro file and perform editconf and then cat? thanks for the suggestions! On Wed, Jul 18, 2012 at 1:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 7:07 AM, Manikam Sadasivam Saravanan wrote: no, water problem is solved, but my protein is still out of the bilayer, When i change:minimize my box vector values and inflate...the protein What does this mean? is packed inside. but now the area per lipid is too low for popc its like 0.148 nm2 After inflation, the area should be huge. What was your command line for InflateGRO? If the protein is not in the desired location, you need to use editconf -center to adjust its coordinates. Make sure it is also within a box that matches that of the lipid bilayer. -Justin On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain
[gmx-users] Problem with Inflategro!!!
Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! ~Saravanan -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
