Re: [gmx-users] Generating topology file for a long polymer chain
Thank you for your help! Best regards, Mahsa On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul wrote: > > > On 8/6/17 8:35 PM, Mahsa E wrote: > >> Hello Justin, >> >> Thank you so much for your reply! >> >> I followed what you suggested. Please correct me if I misunderstood; >> >> 1- I used acpype to generate the parameters (charges, atom types, and >> bonded parameters) for the monomer, which create many files including >> GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files. >> >> 2- Then I build the dimer and used the conformer search in Marvin/Avogadro >> to find the best conformer for the dimer (.xyz or .pdb). >> >> > You'll need to parametrize (at minimum) dihedral terms around the bond > connecting the monomers in the dimer. Finding a single conformer doesn't > give you that information. You need to back up and consult the primary > literature for how your force field should work and how things should be > parametrized (right level of theory, expected level of agreement, etc). > This is not something that either acepype or GROMACS are going to give you; > it usually requires QM work and parameter fitting. > > 3- The missing part for me is from this step. What should I do after >> running acpype for the dimer ? >> how to use the information from previous steps to generate the .itp file >> for a longer chain of polymer (like 25 units)? >> >> > If you've parametrized all possible internal parameters in small model > systems, there's nothing special about larger ones; they're just small > model compounds linked together, so you've already done everything. Just > use pdb2gmx with suitable .rtp files: > > http://www.gromacs.org/Documentation/How-tos/Polymers > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > > == > -- > 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] Generating topology file for a long polymer chain
On 8/6/17 8:35 PM, Mahsa E wrote: Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files. 2- Then I build the dimer and used the conformer search in Marvin/Avogadro to find the best conformer for the dimer (.xyz or .pdb). You'll need to parametrize (at minimum) dihedral terms around the bond connecting the monomers in the dimer. Finding a single conformer doesn't give you that information. You need to back up and consult the primary literature for how your force field should work and how things should be parametrized (right level of theory, expected level of agreement, etc). This is not something that either acepype or GROMACS are going to give you; it usually requires QM work and parameter fitting. 3- The missing part for me is from this step. What should I do after running acpype for the dimer ? how to use the information from previous steps to generate the .itp file for a longer chain of polymer (like 25 units)? If you've parametrized all possible internal parameters in small model systems, there's nothing special about larger ones; they're just small model compounds linked together, so you've already done everything. Just use pdb2gmx with suitable .rtp files: http://www.gromacs.org/Documentation/How-tos/Polymers -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Generating topology file for a long polymer chain
Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files. 2- Then I build the dimer and used the conformer search in Marvin/Avogadro to find the best conformer for the dimer (.xyz or .pdb). 3- The missing part for me is from this step. What should I do after running acpype for the dimer ? how to use the information from previous steps to generate the .itp file for a longer chain of polymer (like 25 units)? Your kind help on this is very much appreciated. Best regards, Mahsa On Sun, Aug 6, 2017 at 2:34 AM, Justin Lemkul wrote: > > > On 8/5/17 8:12 AM, Mahsa E wrote: > >> Dear gmx-users, >> >> I am trying to build a polymer box from scratch and generate the required >> input files. So far, I did these steps: >> 1. built a chain of the polymer >> 2. run ACPYPE to generate the topology file... >> However, since the chain is long, it took so long time with ACPYPE and the >> calculation is timed out without convergence. >> >> - Is it possible to restart the ACPYPE calculation? >> >> I read in some tutorials that it is also possible to run the ACPYPE >> calculations for the monomeric unit instead and repeat its parameters for >> the whole chain. How is it possible? The polymer chain may have a >> conformation with different angles and dihedrals than in the monomer. >> In general, how can I use the topology file of a monomer for the longer >> chain of a polymer ? >> Could you please advise me? >> >> > You parametrize the monomer (charges, atom types, bonded parameters), then > build up by doing, e.g. conformational energy scans of dihedral rotations > between the dimer. That way you can build a proper model of the whole > polymer. Do not try to parametrize an entire polymer at once; you'll end > up with a conformation-specific solution for a given geometry, if you can > even get it to work at all. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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] Generating topology file for a long polymer chain
On 8/5/17 8:12 AM, Mahsa E wrote: Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer ? Could you please advise me? You parametrize the monomer (charges, atom types, bonded parameters), then build up by doing, e.g. conformational energy scans of dihedral rotations between the dimer. That way you can build a proper model of the whole polymer. Do not try to parametrize an entire polymer at once; you'll end up with a conformation-specific solution for a given geometry, if you can even get it to work at all. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Generating topology file for a long polymer chain
Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer? Could you please advise me? Best regards, Mahsa -- 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] Generating topology file for a long polymer chain
Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer ? Could you please advise me? Best regards, Mahsa -- 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.
