Re: [gmx-users] TFE-water simulation
Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] TFE-water simulation
Hello again, That depends on the peptide. There is no general answer. I am starting with a linear conformations, but that's because I'm working with intrinsically disordered proteins. That's as far as I can go regarding telling you about what I'm doing. I'm not at liberty to discuss these things, it's not public yet, sorry. Best regards, João On Fri, Nov 8, 2013 at 11:32 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
Re: [gmx-users] TFE-water simulation
Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
Erratum: Where I wrote I ended up going with the former it should be I ended up going with the latter. /J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] TFE-water simulation
Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? or should I directly add ions to this system and run the production run. Any suggestion is welcome. Thank you. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] TFE-water simulation
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote: Hi all, I have never performed TFE-water simulation therfore I want to know after inserting the peptide in the pre-equilibrated TFE-water mixture, do we need to adjust the number of TFE or water molecules ? That depends on how you constructed the system. genbox will not automatically update the number of TFE, but it can update the number of water molecules if you chose the proper command-line option. Regardless, the [molecules] section of the .top must accurately reflect the contents of the configuration in terms of order and number of molecules. Simple grep statements will let you count how many of each are present. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. Since that file requires the use of the deprecated (i.e. don't use it) gmx.ff force field, I wouldn't. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Sure, if it suits your purpose. See also http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
Hi Justin, Thanks...it was really helpful. I saw the http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site. Now I don't know how to calculate the number of cosolvents (in my case TFE for TFE-water in 1:1 vol). Is there any formula to carry out this calculation. I can follow other mentioned steps. Thanks in advance. On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. Since that file requires the use of the deprecated (i.e. don't use it) gmx.ff force field, I wouldn't. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Sure, if it suits your purpose. See also http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] TFE-water simulation
On 7/17/13 6:26 AM, Archana Sonawani-Jagtap wrote: Hi Justin, Thanks...it was really helpful. I saw the http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site. Now I don't know how to calculate the number of cosolvents (in my case TFE for TFE-water in 1:1 vol). Is there any formula to carry out this calculation. I can follow other mentioned steps. Sure, based on density and the volume of your unit cell, calculating the number of molecules that occupy that space is quite simple. -Justin Thanks in advance. On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. Since that file requires the use of the deprecated (i.e. don't use it) gmx.ff force field, I wouldn't. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Sure, if it suits your purpose. See also http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Can anyone help me out in this regard. Thanks in advance. Regards, Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
