Re: [gmx-users] query regarding itp file
On 5/19/15 10:15 AM, soumadwip ghosh wrote: Thanks Mark for the prompt reply. I can probably make the posre files if required now. But I would be relieved if someone sheds light on the first question that if I already have an .itp file is is necessary to make an entry for the atoms in the aminoacid.rtp file of the corresponding force field? I did not do pdb2gmx to generate the topology of the graphene No. The .rtp entries are only used by pdb2gmx; if you've obtained the topology by other means the .rtp is totally irrelevant. molecule since I obtained the same from PARAMCHEM and the atom types used for graphene are CA and HP which are consistent with some literature. Do I need to modify my aminoacid.rtp file or can I be assured that proper interactions would arise since I am using A BETTER FORCE FIELD (CHARMM 27) for a longer MD simulation (200ns) as per the suggestion by Justin. As far I am concerned the outputs of PARAMCHEM are reliable. I am confused whether I have provided the correct .itp file and whether the expected interaction would arise or not. The parameters of a graphene sheet or a CNT should be very straightforward for an additive model. Whether or not you'll be able to observe the desired outcome depends on whether or not *any* force field can capture that behavior. Materials like graphene and CNT have interesting electronic properties that may play a role here, none of which would be captured by any additive MM model. Use the literature as a guide. If anyone has attempted something similar, use that as inspiration. The CHARMM force fields for nucleic acids (I would recommend CHARMM36 over CHARMM27) are quite good in terms of modeling subtle behavior of nucleic acids. It should be about as good of a model as you'll find. Whether or not the DNA-graphene interaction is described well, that I don't know. -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.
Re: [gmx-users] query regarding itp file
Thanks Mark for the prompt reply. I can probably make the posre files if required now. But I would be relieved if someone sheds light on the first question that if I already have an .itp file is is necessary to make an entry for the atoms in the aminoacid.rtp file of the corresponding force field? I did not do pdb2gmx to generate the topology of the graphene molecule since I obtained the same from PARAMCHEM and the atom types used for graphene are CA and HP which are consistent with some literature. Do I need to modify my aminoacid.rtp file or can I be assured that proper interactions would arise since I am using A BETTER FORCE FIELD (CHARMM 27) for a longer MD simulation (200ns) as per the suggestion by Justin. As far I am concerned the outputs of PARAMCHEM are reliable. I am confused whether I have provided the correct .itp file and whether the expected interaction would arise or not. Waiting for your reply. Regards, Soumadwip Research Fellow IITB India -- 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] query regarding itp file
Hi, You can easily generate position restraints files yourself - have a look at one and learn about the column format from chapter 5. There is also gmx genrestr to help with this - but read the documentation first. Mark On Tue, May 19, 2015 at 2:10 PM soumadwip ghosh wrote: > Hi all, >I have some general doubts about the use of an itp file built by > some software. I am studying the dynamics of a DNA in presence of a > graphene sheet. I am using now the CHARMM27 force field and have obtained a > graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon > atoms and the terminal hydrogen atoms of the graphene sheet have been taken > into account according to the standard CHARMM directory. Now, do I need to > modify my aminoacids.rtp file in order to account for the atoms in the PDB > file? I have not done any pdb2gmx so do I really need to do that step? The > atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms > which describe the graphene framework in addition to other non-bonded > parameters. The equilibration steps are running without any hitches but I > am not getting whether the proper interaction (atomistic) would arise > between graphene and DNA atoms. As suggested by Justin i've switched over > to CHARMM27 force field and am looking at atlest 200 ns of production run. > Another question is, since I have not performed pdb2gmx on graphene, I dont > have a posre_graphene file. Is it gonna create some problem later during > mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre > file for graphene by some other method without doing pdb2gmx if this file > is mandatory? > > Hope I'm not asking for much. > > Regards, > Soumadwip > Research Fellow > IIT Bombay > India > -- > 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.
[gmx-users] query regarding itp file
Hi all, I have some general doubts about the use of an itp file built by some software. I am studying the dynamics of a DNA in presence of a graphene sheet. I am using now the CHARMM27 force field and have obtained a graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon atoms and the terminal hydrogen atoms of the graphene sheet have been taken into account according to the standard CHARMM directory. Now, do I need to modify my aminoacids.rtp file in order to account for the atoms in the PDB file? I have not done any pdb2gmx so do I really need to do that step? The atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms which describe the graphene framework in addition to other non-bonded parameters. The equilibration steps are running without any hitches but I am not getting whether the proper interaction (atomistic) would arise between graphene and DNA atoms. As suggested by Justin i've switched over to CHARMM27 force field and am looking at atlest 200 ns of production run. Another question is, since I have not performed pdb2gmx on graphene, I dont have a posre_graphene file. Is it gonna create some problem later during mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre file for graphene by some other method without doing pdb2gmx if this file is mandatory? Hope I'm not asking for much. Regards, Soumadwip Research Fellow IIT Bombay India -- 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.
