[gmx-users] Bilayer curvature
Dear All, I have set two bilayers: 1. 400 DOPC 2. 320DOPC and 80 Cardiolipin Second one show significant curvature during NPT equilibrium and MD run (not in NVT eq.). Is it normal? For the first bilayer, after adding the protein to the system, here also I can see big curvature in the membrane. Does anybody knows is it normal or something is wrong? Which factors do affect the membrane curvature (like: initial conf., water, ions, box size, equilibration steps, ...)? Thanks, Dariush -- 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: oxidized lipid - Peroxidated lipid
Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661p5008810.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] oxidized lipid - Peroxidated lipid
Hi All, Does anybody know which force filed I can use for oxidized lipid or peroxidated lipid? You can see the below link to get how fatty acid will change by peroxidation: http://en.wikipedia.org/wiki/Lipid_peroxidation If there is not any, what is the suggestion? Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] arrange the atoms in sphere
Hello All, Does anybody have any script to arrange the molecules in the sphere? Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC around). Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: atom numbering
genconf -renumber works well for renumbering. However, after minimization of that renumbered .gro file, I have previous numbering. Dariush On Thu, Aug 16, 2012 at 5:54 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5000267...@n6.nabble.com wrote: On 8/16/12 5:22 PM, dariush wrote: Dear All, I have bilayer system plus two proteins in my system. I numbered residues manually, but after minimization number of residues for both protein 1 and 2 starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it will highlight two res. 3, one in protein 1 and one in protein 2. Do you know how should I figure it out? genconf -renumber -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 list[hidden email]http://user/SendEmail.jtp?type=nodenode=5000267i=0 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5000267i=1. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266p5000267.html To unsubscribe from atom numbering, click herehttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5000266code=ZC5tb2hhbW1hZHlhbmlAZ21haWwuY29tfDUwMDAyNjZ8MTAxNjc4Njk3Ng== . NAMLhttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266p5000297.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: atom numbering
Thank you dear Justin! Dariush On Fri, Aug 17, 2012 at 11:04 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5000298...@n6.nabble.com wrote: On 8/17/12 10:41 AM, dariush wrote: genconf -renumber works well for renumbering. However, after minimization of that renumbered .gro file, I have previous numbering. You always will. The numbering is read from the topology, so simulation output will always be numbered that way and you will have to renumber anything you want to visualize. -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 list[hidden email]http://user/SendEmail.jtp?type=nodenode=5000298i=0 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5000298i=1. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266p5000298.html To unsubscribe from atom numbering, click herehttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5000266code=ZC5tb2hhbW1hZHlhbmlAZ21haWwuY29tfDUwMDAyNjZ8MTAxNjc4Njk3Ng== . NAMLhttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266p5000300.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] atom numbering
Dear All, I have bilayer system plus two proteins in my system. I numbered residues manually, but after minimization number of residues for both protein 1 and 2 starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it will highlight two res. 3, one in protein 1 and one in protein 2. Do you know how should I figure it out? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] PMF - Protein-Mebrane
Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane complex and pull out protein to separate them and calculate the PMF? What would be the difference? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/PMF-Protein-Me-brane-tp569.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Boundary
Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/Boundary-tp4999167.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Simple question (confout)
Hi, Is there any difference between confout.gro file and last frame which we can extract from trajectory? I am thinking they are different!! When I see the trajectory I can see the edge of the well-shaped box, but when I see confout.gro it is not well-shaped and some atoms looks went out out of the box. PS: It does not matter either NPT or NVT was used. Thanks, Dariush -- 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] MARTINI parameters for dodecyl maltoside (DDM)
Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Sun, May 20, 2012 at 1:01 PM, francesco oteri francesco.ot...@gmail.comwrote: Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- 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] MARTINI parameters for dodecyl maltoside (DDM)
Sure, this is the way to make forcefield for your molecule. Also, please check literature. Good luck, Dariush On Mon, May 21, 2012 at 9:26 AM, francesco oteri francesco.ot...@gmail.comwrote: Hi Dariush, I've checked but it seems there no parameters for my detergent. Actully there are parameters for the polar head and the lipidic tail, so it is worth trying to merge them to have the correct representation! Francesco 2012/5/21 Dariush Mohammadyani d.mohammady...@gmail.com Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Sun, May 20, 2012 at 1:01 PM, francesco oteri francesco.ot...@gmail.com wrote: Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] fly some lipids to water
Dear Users, I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a box size 6*6*20 (nm^3). For making this system I used DOPC system with a zero surface tension and then I replaced each DOPC with one CL. Now, I got strange result, after long run, some of lipid (most of them are cardiolipin) fly away from bilayer and come inside the water. Does anybody know what is the problem? How should I fix my system? I am using Coarse grained model using MARTINI force field. Thanks, Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Position Restraints
Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? Regards, Dariush -- 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] Position Restraints
Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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] About Distance.pl script
I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Dariush On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear justin , Thank you for your previous reply When i Download and run Distance.pl script In your website I got the following error readline() on closed filehandle IN at ./Distance.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at ./Distance.pl line 30. How to rectify this error ? Thanks in Advance With regards S.Vidhyasankar -- 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] Box Size in MD
As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 22, 2012 at 12:08 PM, Lara Bunte lara.bu...@yahoo.de wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- 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] clashes
Dear user, When I am using: genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro to add water in a coarse grained system, after running mdrun I am getting Syntax error and it shows maybe the distances are so close or there are some clashes. Do you know how can I figure it out? Or actually if we have some clashes in system how we can correct them? Thanks, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] clashes
Yes, you are right. I made a mistake to write an error: [n0017:07436] *** Process received signal *** [n0017:07436] Signal: Segmentation fault (11) [n0017:07436] Signal code: Address not mapped (1) [n0017:07436] Failing at address: 0x1d620d20 What do you mean for Better energy minimization? Thanks, Dariush On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Dear user, When I am using: genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro to add water in a coarse grained system, after running mdrun I am getting Syntax error and it shows maybe the distances are so close or there are some clashes. I've never heard of mdrun throwing a syntax error. Can you please copy and paste the complete error message from your terminal? Do you know how can I figure it out? Or actually if we have some clashes in system how we can correct them? Better energy minimization typically solves bad atomic clashes. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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] Martini
SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti dinadu...@yahoo.com wrote: Dear Gromacs Specialists, May I ask you to help me for definition of pyrrole, tiofen and aniline in MARTINI coarse-grained force field, Please? I defined them as following: aniline (one benzene ring+NH2) = SC4, SC4, SNd pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1 tiofen (one aromatic ring consists of 4 carbon and one S) = ??? May I ask you to tell me your idea about these molecules, Please? Thank you in advance. Best Regards Dina -- 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] Martini
I think I made a mistake: Aniline: SC4 -SC4 - SNd Pyrrole: SC4 -SNd Tiofen: SC4 - SC5 I am not sure... On Thu, Mar 8, 2012 at 3:24 PM, dina dusti dinadu...@yahoo.com wrote: Dear Dariush, Thank you very much from your response. Then you tell me that the definition of aniline and pyrrole, is correct? Is your mean about SC5 for tiofen means that it is defined as SC4 and SC5 for tiofen? indeed I had doubt about this definition because S is without H in tiofen. May I know your cause for this definition, Please? Best Regards Dina -- *From:* Dariush Mohammadyani d.mohammady...@gmail.com *To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, March 8, 2012 11:24 PM *Subject:* Re: [gmx-users] Martini SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti dinadu...@yahoo.com wrote: Dear Gromacs Specialists, May I ask you to help me for definition of pyrrole, tiofen and aniline in MARTINI coarse-grained force field, Please? I defined them as following: aniline (one benzene ring+NH2) = SC4, SC4, SNd pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1 tiofen (one aromatic ring consists of 4 carbon and one S) = ??? May I ask you to tell me your idea about these molecules, Please? Thank you in advance. Best Regards Dina -- 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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] NAMD file (.inp) convert to GROMACS format
Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] NAMD file (.inp) convert to GROMACS format
Is there any similar script to change it for this reason? On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? You'll have to have a good working knowledge of all file formats involved (which, for Gromacs, requires a thorough read through Chapter 5 of the manual) and design a script that will parse the relevant information from your existing files and write them into Gromacs format. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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] NAMD file (.inp) convert to GROMACS format
Thanks Justin! There is one script in User Contributions page, but it does not work. I totally changed my way, I will use NAMD in this case... On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Is there any similar script to change it for this reason? If there is one that exists, it may have been posted to the User Contributions page of the Gromacs website. If not, maybe someone will post one for you. I've seen this question asked before with no answer, so likely it's time to break out the NAMD and Gromacs manuals in concert with your favorite text editor and scripting language, and have at it. -Justin On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? You'll have to have a good working knowledge of all file formats involved (which, for Gromacs, requires a thorough read through Chapter 5 of the manual) and design a script that will parse the relevant information from your existing files and write them into Gromacs format. -Justin -- ==**__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://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/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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
According your help and pdb2gmx -his -missing I could create input files. Also I used grompp without error. However, for mdrun I got this error: *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Thanks, Dariush On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera kkucz...@ku.edu wrote: Hi Dariush If you are using the CHARMM27 force field, then all topology and parameters are in your share/top/charmm27.ff directory The defined molecules are listed in aminoacids.rtp and force field parameters in numerous other files. CHARMM does not use 'HIS' for histidine, but has HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both. You can either set these isomers by hand - by editing your PDB file or use the 'pdb2gmx -his' option for interactive definition. The bonus of keeping 'HIS' names and interactive setup is that bonds to heme iron will be generated based on the 'specbond.dat' entries, if HIS NE2 nitrogens are close enough to the FE. Krzysztof On 1/10/12 2:40 PM, Dariush Mohammadyani wrote: Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani d.mohammady...@gmail.com wrote: Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu wrote: He must be using an older version of Gromacs. 4.5.4 and lower don't have ACE in charmm27. On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: Here is the blocking group from gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp KK [ ACE ] [ atoms ] CH3 CT3 -0.270 0 HH31HA 0.090 1 HH32HA 0.090 2 HH33HA 0.090 3 C C 0.510 4 O O -0.510 5 [ bonds ] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [ impropers ] C CH3 +N O On 1/6/12 12:40 PM, Peter C. Lai wrote: Corrected bonds section (sorry been up all night) [ ACE ] [ atoms ] CH3CT3-0.270 HH31 HA 0.091 HH32 HA 0.092 HH33 HA 0.093 CC 0.514 OO -0.515 [ bonds ] CH3HH31 CH3HH32 CH3HH33 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. (and the .hdb entry uses HH3 as the base hydrogen name in ACE) On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: Gromos96 53A6 has it. On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by pdb2gmx, but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamersrjham...@wisc.edu wrote: HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use pdb2gmx I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkuljalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 %28540%29%20231-9080 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 -- Robert J. Hamers Wisconsin Distinguished Professor Univ. of Wisconsin-Madison 1101 University Avenue Madison, WI 53706 Ph: 608-262-6371 Web: http://hamers.chem.wisc.edu -- Kind Regards, Dariush
Re: [gmx-users] Cytochrom C
Dear Justin, You are right, I had some warning and with -missing I override them, e.g.: WARNING: atom HA is missing in residue HEM 105 in the pdb file WARNING: atom HB is missing in residue HEM 105 in the pdb file ... 30 missing atoms. I did not know how should figure them out. I am using GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: According your help and pdb2gmx -his -missing I could create input files. Also I used grompp without error. However, for mdrun I got this error: Using the -missing flag is very dangerous. If you're using it to override warnings or errors that pdb2gmx is giving, your simulations will almost certainly be junk because the topology is broken. *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Without seeing your .mdp file and knowing which Gromacs version you're using, there's little anyone can do to help you. The error suggests you're trying to transform a CMAP dihedral using the free energy code, which cannot be done (per the error message). -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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
[gmx-users] Coarse Grained Cytochrom C
Hi all, Has anybody used Coarse grained model for Cytochrome C? I could create a model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), but it does not have HEM and HOH groups. Can anybody help me? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani d.mohammady...@gmail.com wrote: Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu wrote: He must be using an older version of Gromacs. 4.5.4 and lower don't have ACE in charmm27. On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: Here is the blocking group from gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp KK [ ACE ] [ atoms ] CH3 CT3 -0.270 0 HH31HA 0.090 1 HH32HA 0.090 2 HH33HA 0.090 3 C C 0.510 4 O O -0.510 5 [ bonds ] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [ impropers ] C CH3 +N O On 1/6/12 12:40 PM, Peter C. Lai wrote: Corrected bonds section (sorry been up all night) [ ACE ] [ atoms ] CH3CT3-0.270 HH31 HA 0.091 HH32 HA 0.092 HH33 HA 0.093 CC 0.514 OO -0.515 [ bonds ] CH3HH31 CH3HH32 CH3HH33 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. (and the .hdb entry uses HH3 as the base hydrogen name in ACE) On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: Gromos96 53A6 has it. On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by pdb2gmx, but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamersrjham...@wisc.edu wrote: HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use pdb2gmx I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkuljalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Robert J. Hamers Wisconsin Distinguished Professor Univ. of Wisconsin-Madison 1101 University Avenue Madison, WI 53706 Ph: 608-262-6371 Web: http://hamers.chem.wisc.edu -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http
Re: [gmx-users] Cytochrom C
Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. Thanks, Dariush On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Does anybody know where can I find [ HIS ] parameters? HIS is histidine; it's built into every one of the force fields in Gromacs. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] umbrella sampling tutorial quastion
As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha przemekbar...@gmail.comwrote: Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? What I mean, is when we pull molecule A from molecule B, we restrain B to that it does not follow A (by adding pos_res section in .itp file). In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I have got two .itp files for both molecules. Restraining LYS worked well for generating configurations, but failed for umbrella sampling. My molecules (including LYS which was restrained) were flying randomly all over the box which resulted in incorrect PMF courve. So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why? thanks in advance, Przemek -- 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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu wrote: He must be using an older version of Gromacs. 4.5.4 and lower don't have ACE in charmm27. On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: Here is the blocking group from gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp KK [ ACE ] [ atoms ] CH3 CT3 -0.270 0 HH31HA 0.090 1 HH32HA 0.090 2 HH33HA 0.090 3 C C 0.510 4 O O -0.510 5 [ bonds ] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [ impropers ] C CH3 +N O On 1/6/12 12:40 PM, Peter C. Lai wrote: Corrected bonds section (sorry been up all night) [ ACE ] [ atoms ] CH3CT3-0.270 HH31 HA 0.091 HH32 HA 0.092 HH33 HA 0.093 CC 0.514 OO -0.515 [ bonds ] CH3HH31 CH3HH32 CH3HH33 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. (and the .hdb entry uses HH3 as the base hydrogen name in ACE) On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: Gromos96 53A6 has it. On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by pdb2gmx, but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamersrjham...@wisc.edu wrote: HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use pdb2gmx I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkuljalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Robert J. Hamers Wisconsin Distinguished Professor Univ. of Wisconsin-Madison 1101 University Avenue Madison, WI 53706 Ph: 608-262-6371 Web: http://hamers.chem.wisc.edu -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un
Re: [gmx-users] RDF(PMF) and Umbrella sampling
Hi Gavin, A question arose for me: why did you consider the (rate = 0)? Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Justin Just a quick clarification regarding my previous point. With geometry = distance, and pull_dim =Y Y Y . Is the pull_group sampling all dimensions equally (or without prejudice) about pull_init ? And iN your first reply what did you mean about by straight pull ? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for the reply. I wanted my pulling to be free in all directions, that is in the liquid state with no defined reaction coordinate i.e not along a specific axis. This is why I used geometry = distance. Would you agree with this approach? I suppose there is an argument that can be made for a more free approach such as this one, but you're going to get the artifact you observed the instant your pull group moves past a zero COM distance. Whether or not this is a significant problem is something you'll have to determine. -Justin By free I mean. The absolute distance between the COG of the ref group and that of the pull group. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Dear all I have a query regarding umbrella sampling simulations that I have carried out to study a dynamical process of a guest inserting into a host. I always get get a wall tending off to infinity at or just before the zero distance between the two species. The process I describe, for one system in particular, happens readily and I have compared the PMF from a non constrained simulation (via the RDF and reversible work theorem) and the same PMF from a set of umbrella sampling simulations. They agree quite well but in the non constrained simulation I get a minimum practically at zero whereas for the umbrella sampling the minimum is shifted and there is an infinite wall close to zero. This wall is not present from the reversible work theorem. Why the infinite wall? Why does the black histogram not centre around zero. Is this an artefact of the umbrella technique? Please see attached the profile from the umbrella sampling technique, and the corresponding histograms. What's happening is the COM reference distance is changing signs, so you get an artifact. The distance geometry is relatively inflexible and is only suitable for straight pulls of continuously increasing or continuously decreasing COM distance. You should try using the position geometry instead. There are some notes that you may find useful in my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html -Justin Here is an excerpt from one of the umbrella mdp files. pull= umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = tail pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1 pull_nstxout = 150 pull_nstfout = 150 Cheers Gavin -- 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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by pdb2gmx, but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers rjham...@wisc.edu wrote: HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use pdb2gmx I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Robert J. Hamers Wisconsin Distinguished Professor Univ. of Wisconsin-Madison 1101 University Avenue Madison, WI 53706 Ph: 608-262-6371 Web: http://hamers.chem.wisc.edu -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? Thanks, Dariush -- 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
