[gmx-users] .psf and .dcd files
Dear gromacs users I did simulation of protein-ligand by gromacs 4.0.7 with amber 03 forcefield. I need to .psf and .dcd files. can I convert/obtain them? any help will highly appreciated. -- 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] .psf and .dcd files
Hi, You can use wordom to convert .xtc files to .dcd. As for the .psf AFAIK you'll have to work on it yourself using CHARMM or psfgen. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of atila petrosian [atila.petros...@gmail.com] Sent: 19 December 2010 11:04 To: gmx-users@gromacs.org Subject: [gmx-users] .psf and .dcd files Dear gromacs users I did simulation of protein-ligand by gromacs 4.0.7 with amber 03 forcefield. I need to .psf and .dcd files. can I convert/obtain them? any help will highly appreciated. -- 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] .psf and .dcd files
Dear Ran thanks for your reply. Is psfgen a separately 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] .psf and .dcd files
Hi, psfgen is a part of VMD but maybe you can also use it separately. Note that you have to give it the right input and parameters, and I don't know if it works with AMBER-FF. Good luck Ran From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of atila petrosian [atila.petros...@gmail.com] Sent: 19 December 2010 12:36 To: gmx-users@gromacs.org Subject: [gmx-users] .psf and .dcd files Dear Ran thanks for your reply. Is psfgen a separately 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
[gmx-users] RE: multiple dihedrals
In amber dihedral parameters description, IDIVF is the factor by which the torsional barrier (Vn / or force constant) is divided. Usually, this number is 1, but in case of the X used in the dihedral definition like in the case bellow, where X stands for the actual atoms, such as atom1, atom2, atom3 and atom4, there are 3 combinations, giving IDIVF=3. What would be then the right set of entries for such a dihedral in gromacs 4.5? Jarmila On 18/12/2010 1:19 AM, Jarmila Husby wrote: Dear all, Could you please advise me on how to convert a dihedral amber force-field parameter into amberport in Gromacs v 4.5? I have read the mailing list and the manual, so I understand Gmx 4.5 can deal with multiple entries per dihedral, using the type 9 function, instead of accumulating them into a single set of RB parameters. But I do not know how to go about a dihedral with IDIVF number =3, and wild-cards used in the dihedral definition, such as: X - CI - OS - X3 1.1500.0 3.0 What would be the right set of entries for such a dihedral? All suggestions would be much appreciated. What is an IDIVF? Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101218/738988b7/attachment-0001.html -- -- 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! End of gmx-users Digest, Vol 80, Issue 125 ** -- 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] Is there an easy way to increase the energy of bonds, angles, etc?
Arthur Roberts wrote: Hi, all, Is there a way to increase the energy of bonds, angles, etc. without doing it manually? I am looking for a parameter in the mdp file to do this. Your help is greatly appreciated. No. Such a manipulation requires changes to the topology. -Justin Sincerely, Audie Arthur Audie Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 office: 858-822-7804 fax: 858-246-0089 email: aroberts99...@yahoo.com skype=aroberts92122 -- 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: multiple dihedrals
On 19/12/2010 11:13 PM, Jarmila Husby wrote: In amber dihedral parameters description, IDIVF is the factor by which the torsional barrier (Vn / or force constant) is divided. Usually, this number is 1, but in case of the X used in the dihedral definition like in the case bellow, where X stands for the actual atoms, such as atom1, atom2, atom3 and atom4, there are 3 combinations, giving IDIVF=3. I still don't know what all the columns refer to, but GROMACS doesn't do any such gimmicky division... All I can suggest is that you write out the equations both programs claim to implement, and convert the parameters to the right units, and test a zero-step EM for equivalence with both programs. What would be then the right set of entries for such a dihedral in gromacs 4.5? Jarmila On 18/12/2010 1:19 AM, Jarmila Husby wrote: Dear all, Could you please advise me on how to convert a dihedral amber force-field parameter into amberport in Gromacs v 4.5? I have read the mailing list and the manual, so I understand Gmx 4.5 can deal with multiple entries per dihedral, multiple entries refers to the way GROMACS mimics AMBER or CHARMM behaviour regarding accumulating dihedrals described by four specific atom types, usually of different multiplicity. So it's not relevant here. Mark using the type 9 function, instead of accumulating them into a single set of RB parameters. But I do not know how to go about a dihedral with IDIVF number =3, and wild-cards used in the dihedral definition, such as: X - CI - OS - X3 1.1500.0 3.0 What would be the right set of entries for such a dihedral? All suggestions would be much appreciated. What is an IDIVF? Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101218/738988b7/attachment-0001.html -- -- 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! End of gmx-users Digest, Vol 80, Issue 125 ** -- 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] umberella sampling
Dear All and Specially Dear justin After reading umberella sampling tutorial I have afew question. Please let me know their answers. 1-How did you realized(What was your criteria) the range of 0.5 -5 nm is enough? it might be different if you chose 0.2-5 nm.Am I right? 2-The histogram showes a non-overlaping for 1-3 windows,Do I need to run all 23 simulations again with more windows (and small spcing)this time? what is the solution to gain an exact estimation of PMF? 3-Can I select windows in different spacing?in the other words,can I choose small spacing for 1-3 windows and 0.2 nm for others as you chose? Thanks in advance for your reply -- 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] umberella sampling
mohsen ramezanpour wrote: Dear All and Specially Dear justin After reading umberella sampling tutorial I have afew question. Please let me know their answers. 1-How did you realized(What was your criteria) the range of 0.5 -5 nm is enough? it might be different if you chose 0.2-5 nm.Am I right? A PMF is measured over a reaction coordinate. If you change the reaction coordinate, you're measuring something different. For the system in the tutorial, 0.2 nm of COM spacing is not possible. The beta strands cannot be force any closer together. 2-The histogram showes a non-overlaping for 1-3 windows,Do I need to run all 23 simulations again with more windows (and small spcing)this time? what is the solution to gain an exact estimation of PMF? No. If windows do not overlap, then you can either: 1. Extend the simulations in the non-overlapping windows. 2. Add more windows between those that do not overlap. 3. Use a different force constant to allow more mobility within a window. 3-Can I select windows in different spacing?in the other words,can I choose small spacing for 1-3 windows and 0.2 nm for others as you chose? Please refer to the paper cited in the tutorial. We used uneven spacing to actually collect the data, and the reasons for it are discussed. -Justin Thanks in advance for your reply -- 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] water models add polarization, water film
Hi, everyone I have run the 3x3x0.8 water film in 3x3x9 box successful. However, I'd like to add polarization to my water model. Because if i want to investigate solution interface, the ordinary water model cannot reproduce the interface properties well. How can i add polarization water model to Gromacs? do i need to modify the .mdp paremeter? Tiefeng-- 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] water models add polarization, water film
gromacs wrote: Hi, everyone I have run the 3x3x0.8 water film in 3x3x9 box successful. However, I'd like to add polarization to my water model. Because if i want to investigate solution interface, the ordinary water model cannot reproduce the interface properties well. How can i add polarization water model to Gromacs? do i need to modify the .mdp paremeter? Start with the manual, section 4.4, and references therein. Then have a look at sw.itp (in GMXLIB), which is a polarizable water model distributed with Gromacs. -Justin Tiefeng -- 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] Re: water models add polarization, water film
Hi, everyone I have run the 3x3x0.8 water film in 3x3x9 box successful. It is a time for me to proudly ask: Was i right before? ... However, I'd like to add polarization to my water model. Because if i want to investigate solution interface, the ordinary water model cannot reproduce the interface properties well. How can i add polarization water model to Gromacs? do i need to modify the .mdp paremeter? You should modify topology file. See SW.ITP in the standard gromacs topology folder as an example. Or if you're lazy, just use this water model for your study... I am not sure that polarizable waters are always better to simulate interface properties than conventional ones. Dr. Vitaly V. Chaban Rochester, U.S.A. -- 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] (no subject)
http://www.ergo2go.nl/shop/images/mysite.html -- 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] reagarding polarisable force field in gromacs
Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. thanks in advance , shree -- 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] reagarding polarisable force field in gromacs
sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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] reagarding polarisable force field in gromacs
Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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] reagarding polarisable force field in gromacs
What is it exactly that you don't get? You need to provide more details and put your question into context. Then people can give you more directed responses that will help you. Otherwise it is too open ended. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of sreelakshmi ramesh Sent: Monday, 20 December 2010 2:58 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] reagarding polarisable force field in gromacs Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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] reagarding polarisable force field in gromacs
sreelakshmi ramesh wrote: Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. Then what you should have found is that there are no polarizable force fields in Gromacs, but it may be possible to implement one using the contents of sw.itp (a simple water model) as a template. The files you would need to create (and their contents) will be described in Chapters 4 and 5 of the manual. Beyond that, you would have to be very specific as to the part(s) of implementation with which you're having difficulty. Otherwise, you'll just get pointed to the manual. -Justin On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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
Re: [gmx-users] reagarding polarisable force field in gromacs
Dear justin , I am using tip4p water model for my work and i have the tip4p.itp file if i just wanted polarisable force field so as you told me i have the tip4p.itp file.should i modify this file or the force field.itp file reagrds, shree On Mon, Dec 20, 2010 at 9:33 AM, Justin A. Lemkul jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. Then what you should have found is that there are no polarizable force fields in Gromacs, but it may be possible to implement one using the contents of sw.itp (a simple water model) as a template. The files you would need to create (and their contents) will be described in Chapters 4 and 5 of the manual. Beyond that, you would have to be very specific as to the part(s) of implementation with which you're having difficulty. Otherwise, you'll just get pointed to the manual. -Justin On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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 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] reagarding polarisable force field in gromacs
sreelakshmi ramesh wrote: Dear justin , I am using tip4p water model for my work and i have the tip4p.itp file if i just wanted polarisable force field so as you told me i have the tip4p.itp file.should i modify this file or the force field.itp file As I suggested before, you will find some useful information in sw.itp, which, conveniently, is a polarizable water model. If you want to continue to receive free help, please apply what has been offered previously and ask specific questions when you run into problems. -Justin reagrds, shree On Mon, Dec 20, 2010 at 9:33 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. Then what you should have found is that there are no polarizable force fields in Gromacs, but it may be possible to implement one using the contents of sw.itp (a simple water model) as a template. The files you would need to create (and their contents) will be described in Chapters 4 and 5 of the manual. Beyond that, you would have to be very specific as to the part(s) of implementation with which you're having difficulty. Otherwise, you'll just get pointed to the manual. -Justin On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: sreelakshmi ramesh wrote: Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. Start by reading the manual. All of the force fields included in Gromacs are described. Polarizability is discussed in section 4.4, mostly in relation to water models. -Justin thanks in advance , shree -- 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 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.
[gmx-users] Reg: fatal error pdb2gmx
Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAACAB CABCAC CACCAD CADCAE CAECAF [ angles ] CAACABCAC CABCACCAD CACCADCAE CADCAECAF [ dihedrals ] CAACABCACCAD CABCACCADCAE CACCADCAECAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution ( http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- Regards Vinoth -- 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] Reg: fatal error pdb2gmx
vinothkumar mohanakrishnan wrote: Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAACAB CABCAC CACCAD CADCAE CAECAF [ angles ] CAACABCAC CABCACCAD CACCADCAE CADCAECAF [ dihedrals ] CAACABCACCAD CABCACCADCAE CACCADCAECAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution (http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- There is something wrong with the format of your .rtp file. Unfortunately, the error message in this case is not particularly helpful. Based on the residue and atom naming, it appears that you're trying to interface some sort of PRODRG output with OPLS-AA. Doing so is fundamentally flawed, mostly because PRODRG gives GROMOS-compatible topologies (often poor ones, at that). Presumably, you have introduced new atom types (opls_966/967) corresponding to some united-atom C type. OPLS-AA is an all-atom force field, so introducing a united-atom hexane topology is simply wrong, unless you have somehow demonstrated that a united-atom model behaves properly and you have done the thorough work of parameterizing this model. -Justin Regards Vinoth -- 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] Reg: fatal error pdb2gmx
Hi Justin I had taken United atom pdb file form PRODRG and i want to use OPLS-UA force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc. Regards Vinoth On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAACAB CABCAC CACCAD CADCAE CAECAF [ angles ] CAACABCAC CABCACCAD CACCADCAE CADCAECAF [ dihedrals ] CAACABCACCAD CABCACCADCAE CACCADCAECAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution ( http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- There is something wrong with the format of your .rtp file. Unfortunately, the error message in this case is not particularly helpful. Based on the residue and atom naming, it appears that you're trying to interface some sort of PRODRG output with OPLS-AA. Doing so is fundamentally flawed, mostly because PRODRG gives GROMOS-compatible topologies (often poor ones, at that). Presumably, you have introduced new atom types (opls_966/967) corresponding to some united-atom C type. OPLS-AA is an all-atom force field, so introducing a united-atom hexane topology is simply wrong, unless you have somehow demonstrated that a united-atom model behaves properly and you have done the thorough work of parameterizing this model. -Justin Regards Vinoth -- 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] Reg: fatal error pdb2gmx
vinothkumar mohanakrishnan wrote: Hi Justin I had taken United atom pdb file form PRODRG and i want to use OPLS-UA Interesting choice. That's an antiquated force field... force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc. To create a topology for a simple six-atom molecule, pdb2gmx is unnecessary. Just write the topology by hand. You've effectively already done so. Or, you can try to troubleshoot an unfortunately cryptic error message. -Justin Regards Vinoth On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAACAB CABCAC CACCAD CADCAE CAECAF [ angles ] CAACABCAC CABCACCAD CACCADCAE CADCAECAF [ dihedrals ] CAACABCACCAD CABCACCADCAE CACCADCAECAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution (http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- There is something wrong with the format of your .rtp file. Unfortunately, the error message in this case is not particularly helpful. Based on the residue and atom naming, it appears that you're trying to interface some sort of PRODRG output with OPLS-AA. Doing so is fundamentally flawed, mostly because PRODRG gives GROMOS-compatible topologies (often poor ones, at that). Presumably, you have introduced new atom types (opls_966/967) corresponding to some united-atom C type. OPLS-AA is an all-atom force field, so introducing a united-atom hexane topology is simply wrong, unless you have somehow demonstrated that a united-atom model behaves properly and you have done the thorough work of parameterizing this model. -Justin Regards Vinoth -- 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 --
Re: [gmx-users] Reg: fatal error pdb2gmx
Even though the UA force field is outdated i want to use that and try to rectify the cryptic error message that keeps coming. Thank you very much for your suggestions Justin. Regards Vinoth On Mon, Dec 20, 2010 at 11:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi Justin I had taken United atom pdb file form PRODRG and i want to use OPLS-UA Interesting choice. That's an antiquated force field... force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc. To create a topology for a simple six-atom molecule, pdb2gmx is unnecessary. Just write the topology by hand. You've effectively already done so. Or, you can try to troubleshoot an unfortunately cryptic error message. -Justin Regards Vinoth On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opls_967 0 2 CAE opls_967 0 2 [ bonds ] CAACAB CABCAC CACCAD CADCAE CAECAF [ angles ] CAACABCAC CABCACCAD CACCADCAE CADCAECAF [ dihedrals ] CAACABCACCAD CABCACCADCAE CACCADCAECAF but i get the error message as given below and it doesn't generate any .top and .gro file . I searched the mailing list and found a similar post but there is no solution ( http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated. Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 All occupancies are one Opening library file ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- There is something wrong with the format of your .rtp file. Unfortunately, the error message in this case is not particularly helpful. Based on the residue and atom naming, it appears that you're trying to interface some sort of PRODRG output with OPLS-AA. Doing so is fundamentally flawed, mostly because PRODRG gives GROMOS-compatible topologies (often poor ones, at that). Presumably, you have introduced new atom types (opls_966/967) corresponding to some united-atom C type. OPLS-AA is an all-atom force field, so introducing a united-atom hexane topology is simply wrong, unless you have somehow demonstrated that a united-atom model behaves properly and you have done the thorough work of parameterizing this model. -Justin Regards Vinoth -- Justin A. Lemkul Ph.D. Candidate ICTAS
