Re: [gmx-users] I: How to rolled up a polymer chain
On 9/25/14 4:57 AM, marcello cammarata wrote: Hi to all, in order to find the position tangled of a polymer chain, i tried to follow the indication of hte page Polymer reported in the gromacs guide on line. i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and i save the file on the folder oplsaa, also i created a file PE.pdb as reported in the same page, with the indication for create a chain of polyetilene of 6 monomers, and i saved this last file in the folder gromacs/src/ You shouldn't be messing with anything in the src folder; that's the source code, not the installed Gromacs. Nothing you do here will have any effect. I start with the command pdb2gmx -f PE.pdb i select the force field as 14 OPLS-AA/L i select none as water model (bacause it is a single polymer chain) I got the message "residue ethB non found in the residue topology database, aminoacid.r2b" I read that the software tried to open other files as aminoacids.rpt aminoacids.hdb and it doen't found the residue. A that point i thought to modify the files aminoacids.rpt and aminoacids.rdb by write down what was in the files oplsaa.rtp and oplsaa.hdb in the files aminoacids.rtp and aminoacids.hdb. Follow, I run the software with the comand pdb2gmx -f PE.pdb wwith same force field and same none water. i got the same message:"residue ethB non found in the residue topology database, aminoacid.r2b" Questions are: how i can do for load that residue? What do you suggest to do for induce the software to load my residue? A few things: 1. The file names in the posted example are outdated, but it should be straightforward to see what the new file names are in the reorganized force field files. 2. The best approach is not to create files from scratch (especially if you are unfamiliar with how all of this works), but rather to extend the existing force field. Make a local copy of the oplsaa.ff directory in your working directory. Add residues to its .rtp file, .hdb entries, etc. as needed in those files. Use this modified force field when running pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Hi to all, in order to find the position tangled of a polymer chain, i tried to follow the indication of hte page Polymer reported in the gromacs guide on line. i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and i save the file on the folder oplsaa, also i created a file PE.pdb as reported in the same page, with the indication for create a chain of polyetilene of 6 monomers, and i saved this last file in the folder gromacs/src/ I start with the command pdb2gmx -f PE.pdb i select the force field as 14 OPLS-AA/L i select none as water model (bacause it is a single polymer chain) I got the message "residue ethB non found in the residue topology database, aminoacid.r2b" I read that the software tried to open other files as aminoacids.rpt aminoacids.hdb and it doen't found the residue. A that point i thought to modify the files aminoacids.rpt and aminoacids.rdb by write down what was in the files oplsaa.rtp and oplsaa.hdb in the files aminoacids.rtp and aminoacids.hdb. Follow, I run the software with the comand pdb2gmx -f PE.pdb wwith same force field and same none water. i got the same message:"residue ethB non found in the residue topology database, aminoacid.r2b" Questions are: how i can do for load that residue? What do you suggest to do for induce the software to load my residue? Bests. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Mercoledì 24 Settembre 2014 3:45, Mohd Farid Ismail ha scritto: I think you should take Dr. Lemkul's advice, that is to try with a small molecule system first. In general, from what I've learned, you first need to create the .rtp file, and put it in the oplsaa.ff directory. This is all assuming you want to use oplsaa forcefield. Check out the .rtp file format in the manual, or look at the aminoacid.rtp file in the oplsaa.ff directory. Then try pdb2gmx again. But, I'm wondering whether what you're trying to achieve feasible? IIRC I saw a review by Gary Grest and Kurt Kremer that for PE, it takes hundreds of nano seconds for 10 PE chains to equilibrate (for all atom model). Who knows how long it would take for your system, polyamide. Even with coarse-grain forcefield, it should take forever to equilibrate polymer melts. Maybe this is a long time scale project (years before your get results)? And if you want to use CG models, then there's no need to create detailed atomistic model with avogadro. And there are other software that does this better, hoomd or lammps come to mind. By no means I am trying to discourage you. Someone has to try this. The more people work on this, the more chances someone will come up with the answer. I just wonder whether you actually have considered the issues with this kind of system and found a solution. --Farid 24.09.2014, 02:16, "marcello cammarata" : yes, > >i need yto know how it go to tangled, related with the lenght of chain, the >number of chains in volume unit. >For now the problem is that when i run pdd2gmx, i don't choose any solvent, >because there isn't eny solvent, i choose only a kind of force field present >in the database software. but each time it ask me for the LIG. > >I have a bdp file with the chain, made by me. > > > >MARCELLO CAMMARATA >Ing., Ph.D., > > > 3208790796 > > > > >Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail > ha scritto: > > > >Can I ask you something. What do you mean by "rolled up"? Do you mean create >the tangled conformation of polymer chains? > >--Farid > > >22.09.2014, 20:46, "marcello cammarata" : >> Hi, >> i had checked all the archives, i have read about 100posts in the last 2 >> month. >> Nobody have problem similar to mine. >> Problem for me are Two. >> 1- instead i am a doctor, i am not able to find the right advice at your >> site. >> 2- In your site there is no space for begginer user. >> >> The main pages where i checked are: >> Residue >> Chain >> Polyethylene (PE) simulations in Gromacs - please! >> .rtp File >> Force Fields >> Adding a Residue to a Force Field >> Modifying a force field >> >> But i don't have find any suggestion for my problem. >> Is there an other blog, that i can't see. >> i have several of problem with Gromacs, >> - in Cygwin it doen't work, i got a "bash" comand >> - the topology need a lig parameters. >> >> one more time, below there is my post. I wpould like if you can help me to >> solve this question, instead i can try to use an othere MD software. >> >> MARCELLO CAMMARATA >> Ing., Ph.D., >> >> 3208790796 >> >> Il Lunedì 22 Settembre 2014 14:20, marcello cammarata >> ha scritto: >> >> My goal, for now, is to model a polimer (nylon-6) chain, and to find the >> equilibrium position of the chain considering the capacity to be rolled up >> itself. >> I had create a pdb file using Avogadro software, but when i go to gromacs to >> input the >> data using the function pdb2gmx And indipendently of the force field that i >> choos
Re: [gmx-users] I: How to rolled up a polymer chain
On 9/23/14 7:43 PM, marcello cammarata wrote: Do you know how change force field? how i can do this? Everything you need to create the polymer is described here: http://www.gromacs.org/Documentation/How-tos/Polymers The page includes a link to a discussion that goes step-by-step through how to set up a PE system. Anything else is covered in the pages that have been posted before, notably "Adding a residue to a force field." so the goal can be this, i can consider two molecules asmetilene or ethilene or butene, and i want kwon by appling a set of force field the mutual distance beetween the two groups. This doesn't make most sense. How i can do this? how is possible to set force field? Try the example posted above. See if you can make something simple work. Then, based on what you learn, try something more complicated or otherwise different. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
The first couple of responses you received to your question provided the resources in order to do what you are looking to do, and answered the exact questions you have asked here. Go back and have a look at those and follow the links provided. They are written in general terms though, since they are written for everyone, not for something as specific as what you are trying to do. It is important to note that what you are looking to do is not easy, especially for someone that is new to MD and a software package. If you want to get something out that is useful and not a waste of your time, I would suggest you find someone in the know to collaborate with. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > marcello cammarata > Sent: Wednesday, 24 September 2014 9:43 AM > To: Johnny Lu; gmx-us...@gromacs.org > Subject: Re: [gmx-users] I: How to rolled up a polymer chain > > Do you know how change force field? > how i can do this? > so the goal can be this, i can consider two molecules asmetilene or > ethilene or butene, and i want kwon by appling a set of force field the > mutual distance beetween the two groups. > > How i can do this? > how is possible to set force field? > > bests > > > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > > > Il Mercoledì 24 Settembre 2014 0:41, Johnny Lu > ha scritto: > > > > Molecular dynamics software, like gromacs, use a set of rules to > simulate the real world. > This set of rules is a force-field. > > Force field is the simplified physical rules of the real world that are > hopefully approximately right. > > Such simplified rules usually can not describe everything in the real > world. > Usually people have to extend the forcefield by finding the correct > parameters (using spectrums from experiments, quantum mechanical > calculation... just the way that people used to make a force field in > the first place) to simulate drugs within proteins. > > You can either extend the force field; so that the force-field describe > polyethylene. > Or use an existing force field that can describe polyethylene. > > So far, I guess the force-fields implemented in gromacs can not > describe polyethylene (unless you change the force-fields). > > > > On Tue, Sep 23, 2014 at 2:15 PM, marcello cammarata > wrote: > > yes, > > > >i need yto know how it go to tangled, related with the lenght of > chain, the number of chains in volume unit. > >For now the problem is that when i run pdd2gmx, i don't choose any > solvent, because there isn't eny solvent, i choose only a kind of force > field present in the database software. but each time it ask me for the > LIG. > > > >I have a bdp file with the chain, made by me. > > > > > > > >MARCELLO CAMMARATA > >Ing., Ph.D., > > > > 3208790796 > > > > > >Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail > ha scritto: > > > > > > > > > >Can I ask you something. What do you mean by "rolled up"? Do you > mean create the tangled conformation of polymer chains? > > > >--Farid > > > > > >22.09.2014, 20:46, "marcello cammarata" : > >> Hi, > >> i had checked all the archives, i have read about 100posts in the > last 2 month. > >> Nobody have problem similar to mine. > >> Problem for me are Two. > >> 1- instead i am a doctor, i am not able to find the right advice at > your site. > >> 2- In your site there is no space for begginer user. > >> > >> The main pages where i checked are: > >> Residue > >> Chain > >> Polyethylene (PE) simulations in Gromacs - please! > >> .rtp File > >> Force Fields > >> Adding a Residue to a Force Field > >> Modifying a force field > >> > >> But i don't have find any suggestion for my problem. > >> Is there an other blog, that i can't see. > >> i have several of problem with Gromacs, > >> - in Cygwin it doen't work, i got a "bash" comand > >> - the topology need a lig parameters. > >> > >> one more time, below there is my post. I wpould like if you can help &
Re: [gmx-users] I: How to rolled up a polymer chain
Do you know how change force field? how i can do this? so the goal can be this, i can consider two molecules asmetilene or ethilene or butene, and i want kwon by appling a set of force field the mutual distance beetween the two groups. How i can do this? how is possible to set force field? bests MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Mercoledì 24 Settembre 2014 0:41, Johnny Lu ha scritto: Molecular dynamics software, like gromacs, use a set of rules to simulate the real world. This set of rules is a force-field. Force field is the simplified physical rules of the real world that are hopefully approximately right. Such simplified rules usually can not describe everything in the real world. Usually people have to extend the forcefield by finding the correct parameters (using spectrums from experiments, quantum mechanical calculation... just the way that people used to make a force field in the first place) to simulate drugs within proteins. You can either extend the force field; so that the force-field describe polyethylene. Or use an existing force field that can describe polyethylene. So far, I guess the force-fields implemented in gromacs can not describe polyethylene (unless you change the force-fields). On Tue, Sep 23, 2014 at 2:15 PM, marcello cammarata wrote: yes, > >i need yto know how it go to tangled, related with the lenght of chain, the >number of chains in volume unit. >For now the problem is that when i run pdd2gmx, i don't choose any solvent, >because there isn't eny solvent, i choose only a kind of force field present >in the database software. but each time it ask me for the LIG. > >I have a bdp file with the chain, made by me. > > > >MARCELLO CAMMARATA >Ing., Ph.D., > > 3208790796 > > >Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail > ha scritto: > > > > >Can I ask you something. What do you mean by "rolled up"? Do you mean create >the tangled conformation of polymer chains? > >--Farid > > >22.09.2014, 20:46, "marcello cammarata" : >> Hi, >> i had checked all the archives, i have read about 100posts in the last 2 >> month. >> Nobody have problem similar to mine. >> Problem for me are Two. >> 1- instead i am a doctor, i am not able to find the right advice at your >> site. >> 2- In your site there is no space for begginer user. >> >> The main pages where i checked are: >> Residue >> Chain >> Polyethylene (PE) simulations in Gromacs - please! >> .rtp File >> Force Fields >> Adding a Residue to a Force Field >> Modifying a force field >> >> But i don't have find any suggestion for my problem. >> Is there an other blog, that i can't see. >> i have several of problem with Gromacs, >> - in Cygwin it doen't work, i got a "bash" comand >> - the topology need a lig parameters. >> >> one more time, below there is my post. I wpould like if you can help me to >> solve this question, instead i can try to use an othere MD software. >> >> MARCELLO CAMMARATA >> Ing., Ph.D., >> >> 3208790796 >> >> Il Lunedì 22 Settembre 2014 14:20, marcello cammarata >> ha scritto: >> >> My goal, for now, is to model a polimer (nylon-6) chain, and to find the >> equilibrium position of the chain considering the capacity to be rolled up >> itself. >> I had create a pdb file using Avogadro software, but when i go to gromacs to >> input the >> data using the function pdb2gmx And indipendently of the force field that i >> choose i get :that "Residue LIG not found". >> >> How to solve this? >> thanks >> >> MARCELLO CAMMARATA >> Ing., Ph.D., >> >> 3208790796 >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > >-- >Mohd Farid Ismail >mohd.farid.ism...@yandex.com >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] I: How to rolled up a polymer chain
Molecular dynamics software, like gromacs, use a set of rules to simulate the real world. This set of rules is a force-field. Force field is the simplified physical rules of the real world that are hopefully approximately right. Such simplified rules usually can not describe everything in the real world. Usually people have to extend the forcefield by finding the correct parameters (using spectrums from experiments, quantum mechanical calculation... just the way that people used to make a force field in the first place) to simulate drugs within proteins. You can either extend the force field; so that the force-field describe polyethylene. Or use an existing force field that can describe polyethylene. So far, I guess the force-fields implemented in gromacs can not describe polyethylene (unless you change the force-fields). On Tue, Sep 23, 2014 at 2:15 PM, marcello cammarata wrote: > yes, > > i need yto know how it go to tangled, related with the lenght of chain, > the number of chains in volume unit. > For now the problem is that when i run pdd2gmx, i don't choose any > solvent, because there isn't eny solvent, i choose only a kind of force > field present in the database software. but each time it ask me for the LIG. > > I have a bdp file with the chain, made by me. > > > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > > > Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail < > mohd.farid.ism...@yandex.com> ha scritto: > > > > Can I ask you something. What do you mean by "rolled up"? Do you mean > create the tangled conformation of polymer chains? > > --Farid > > > 22.09.2014, 20:46, "marcello cammarata" : > > Hi, > > i had checked all the archives, i have read about 100posts in the last > 2 month. > > Nobody have problem similar to mine. > > Problem for me are Two. > > 1- instead i am a doctor, i am not able to find the right advice at your > site. > > 2- In your site there is no space for begginer user. > > > > The main pages where i checked are: > > Residue > > Chain > > Polyethylene (PE) simulations in Gromacs - please! > > .rtp File > > Force Fields > > Adding a Residue to a Force Field > > Modifying a force field > > > > But i don't have find any suggestion for my problem. > > Is there an other blog, that i can't see. > > i have several of problem with Gromacs, > > - in Cygwin it doen't work, i got a "bash" comand > > - the topology need a lig parameters. > > > > one more time, below there is my post. I wpould like if you can help me > to solve this question, instead i can try to use an othere MD software. > > > > MARCELLO CAMMARATA > > Ing., Ph.D., > > > > 3208790796 > > > > Il Lunedì 22 Settembre 2014 14:20, marcello cammarata < > mstaxmarce...@yahoo.it> ha scritto: > > > > My goal, for now, is to model a polimer (nylon-6) chain, and to find the > equilibrium position of the chain considering the capacity to be rolled up > itself. > > I had create a pdb file using Avogadro software, but when i go to > gromacs to input the > > data using the function pdb2gmx And indipendently of the force field > that i > > choose i get :that "Residue LIG not found". > > > > How to solve this? > > thanks > > > > MARCELLO CAMMARATA > > Ing., Ph.D., > > > > 3208790796 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Mohd Farid Ismail > mohd.farid.ism...@yandex.com > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
yes, i need yto know how it go to tangled, related with the lenght of chain, the number of chains in volume unit. For now the problem is that when i run pdd2gmx, i don't choose any solvent, because there isn't eny solvent, i choose only a kind of force field present in the database software. but each time it ask me for the LIG. I have a bdp file with the chain, made by me. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail ha scritto: Can I ask you something. What do you mean by "rolled up"? Do you mean create the tangled conformation of polymer chains? --Farid 22.09.2014, 20:46, "marcello cammarata" : > Hi, > i had checked all the archives, i have read about 100posts in the last 2 > month. > Nobody have problem similar to mine. > Problem for me are Two. > 1- instead i am a doctor, i am not able to find the right advice at your site. > 2- In your site there is no space for begginer user. > > The main pages where i checked are: > Residue > Chain > Polyethylene (PE) simulations in Gromacs - please! > .rtp File > Force Fields > Adding a Residue to a Force Field > Modifying a force field > > But i don't have find any suggestion for my problem. > Is there an other blog, that i can't see. > i have several of problem with Gromacs, > - in Cygwin it doen't work, i got a "bash" comand > - the topology need a lig parameters. > > one more time, below there is my post. I wpould like if you can help me to > solve this question, instead i can try to use an othere MD software. > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > > Il Lunedì 22 Settembre 2014 14:20, marcello cammarata > ha scritto: > > My goal, for now, is to model a polimer (nylon-6) chain, and to find the > equilibrium position of the chain considering the capacity to be rolled up > itself. > I had create a pdb file using Avogadro software, but when i go to gromacs to > input the > data using the function pdb2gmx And indipendently of the force field that i > choose i get :that "Residue LIG not found". > > How to solve this? > thanks > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Mohd Farid Ismail mohd.farid.ism...@yandex.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Can I ask you something. What do you mean by "rolled up"? Do you mean create the tangled conformation of polymer chains? --Farid 22.09.2014, 20:46, "marcello cammarata" : > Hi, > i had checked all the archives, i have read about 100posts in the last 2 > month. > Nobody have problem similar to mine. > Problem for me are Two. > 1- instead i am a doctor, i am not able to find the right advice at your site. > 2- In your site there is no space for begginer user. > > The main pages where i checked are: > Residue > Chain > Polyethylene (PE) simulations in Gromacs - please! > .rtp File > Force Fields > Adding a Residue to a Force Field > Modifying a force field > > But i don't have find any suggestion for my problem. > Is there an other blog, that i can't see. > i have several of problem with Gromacs, > - in Cygwin it doen't work, i got a "bash" comand > - the topology need a lig parameters. > > one more time, below there is my post. I wpould like if you can help me to > solve this question, instead i can try to use an othere MD software. > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > > Il Lunedì 22 Settembre 2014 14:20, marcello cammarata > ha scritto: > > My goal, for now, is to model a polimer (nylon-6) chain, and to find the > equilibrium position of the chain considering the capacity to be rolled up > itself. > I had create a pdb file using Avogadro software, but when i go to gromacs to > input the > data using the function pdb2gmx And indipendently of the force field that i > choose i get :that "Residue LIG not found". > > How to solve this? > thanks > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Mohd Farid Ismail mohd.farid.ism...@yandex.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Hi. I noticed mis-spellings in manual of another MD software that persisted throughout its versions. Googling for "polyethylene simulation" gave this article as first result: http://arxiv.org/pdf/1401.4295v1.pdf, which use lammps. I'm not sure about the availability, accuracy, and computation cost of the force field that they talk about. Personally, I guess simulation is like a film or drama. Using the right setup and looking from the correct angle (like from the front of the stage) give reasonable results. Using the wrong setup, or looking from the wrong direction (like from the side-way of the stage) can give wrong result. On Mon, Sep 22, 2014 at 8:50 AM, Justin Lemkul wrote: > > > On 9/22/14 8:46 AM, marcello cammarata wrote: > >> >> Hi, >> i had checked all the archives, i have read about 100posts in the last >> 2 month. >> Nobody have problem similar to mine. >> Problem for me are Two. >> 1- instead i am a doctor, i am not able to find the right advice at your >> site. >> 2- In your site there is no space for begginer user. >> >> The main pages where i checked are: >> Residue >> Chain >> Polyethylene (PE) simulations in Gromacs - please! >> .rtp File >> Force Fields >> Adding a Residue to a Force Field >> Modifying a force field >> >> > All the information you need are in the above pages. You may want to do > some simple tutorial material on known species before diving into something > that requires detailed knowledge of Gromacs file formats and topology > organization. There is basically a how-to at http://www.gromacs.org/ > Documentation/How-tos/Polymers > > But i don't have find any suggestion for my problem. >> Is there an other blog, that i can't see. >> i have several of problem with Gromacs, >> - in Cygwin it doen't work, i got a "bash" comand >> - the topology need a lig parameters. >> >> one more time, below there is my post. I wpould like if you can help me >> to solve this question, instead i can try to use an othere MD software. >> >> > You'll encounter the same problem in just about every software you use. > If you're using a molecule that is unknown to the force field, you're going > to have to modify force field and/or topology files in some way. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
On 9/22/14 8:46 AM, marcello cammarata wrote: Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field All the information you need are in the above pages. You may want to do some simple tutorial material on known species before diving into something that requires detailed knowledge of Gromacs file formats and topology organization. There is basically a how-to at http://www.gromacs.org/Documentation/How-tos/Polymers But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a "bash" comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. You'll encounter the same problem in just about every software you use. If you're using a molecule that is unknown to the force field, you're going to have to modify force field and/or topology files in some way. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Add the parameters for LIG residue in force filed. In that give information about the LIG in rtp file nonbonded file bonded file I think then it will work. On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata wrote: > > Hi, > i had checked all the archives, i have read about 100posts in the last 2 > month. > Nobody have problem similar to mine. > Problem for me are Two. > 1- instead i am a doctor, i am not able to find the right advice at your > site. > 2- In your site there is no space for begginer user. > > The main pages where i checked are: > Residue > Chain > Polyethylene (PE) simulations in Gromacs - please! > .rtp File > Force Fields > Adding a Residue to a Force Field > Modifying a force field > > But i don't have find any suggestion for my problem. > Is there an other blog, that i can't see. > i have several of problem with Gromacs, > - in Cygwin it doen't work, i got a "bash" comand > - the topology need a lig parameters. > > one more time, below there is my post. I wpould like if you can help me to > solve this question, instead i can try to use an othere MD software. > > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > > > Il Lunedì 22 Settembre 2014 14:20, marcello cammarata < > mstaxmarce...@yahoo.it> ha scritto: > > > > > > My goal, for now, is to model a polimer (nylon-6) chain, and to find the > equilibrium position of the chain considering the capacity to be rolled up > itself. > I had create a pdb file using Avogadro software, but when i go to gromacs > to input the > data using the function pdb2gmx And indipendently of the force field that > i > choose i get :that "Residue LIG not found". > > How to solve this? > thanks > > > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- regards M.SathishKumar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] I: How to rolled up a polymer chain
Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a "bash" comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Lunedì 22 Settembre 2014 14:20, marcello cammarata ha scritto: My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself. I had create a pdb file using Avogadro software, but when i go to gromacs to input the data using the function pdb2gmx And indipendently of the force field that i choose i get :that "Residue LIG not found". How to solve this? thanks MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
