Thank you for reply.. But how can i identify the molecule as methylamine (for example) since in the .rtp the molecule type is written as [MAM1] [ MAM1 ] [ atoms ] N1 NG321 -0.990 0 C1 CG3AM2 -0.060 1 HN1 HGPAM2 0.390 2 HN2 HGPAM2 0.390 3 HC1 HGAAM2 0.090 4 HC2 HGAAM2 0.090 5 HC3 HGAAM2 0.090 6 [ bonds ] N1 C1 N1 HN1 N1 HN2 C1 HC1 C1 HC2 C1 HC3 Is thr any hint such tht i can identify the molecule type written in .rtp file.?? Or should i manually find it out..??... but in case of Glycine the molecule type is [GLY] which is easy to find.... How can i solve this issue..??
Thank you... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > Hello all. > > 1] I want to knw how the charges are designated/assigned for the each > atoms > > in molecule in the .rtp file. ie., as example for methylamine in CHARMM > > FF:- > > > > [ MAM1 ] > > [ atoms ] > > N1 NG321 -0.990 0 > > C1 CG3AM2 -0.060 1 > > HN1 HGPAM2 0.390 2 > > HN2 HGPAM2 0.390 3 > > HC1 HGAAM2 0.090 4 > > HC2 HGAAM2 0.090 5 > > HC3 HGAAM2 0.090 6 > > [ bonds ] > > N1 C1 > > N1 HN1 > > N1 HN2 > > C1 HC1 > > C1 HC2 > > C1 HC3 > > ie how are the charges -0.990, -0.060, 0.390 etc., are assigned... > > > > The parameterization methodology is unique to each force field, and perhaps > to each tool that generates compatible topologies. You need to read that > documentation and literature to understand how they were derived. > > > > 2] and if i get the topology/itp file from the automated topology builder > > as in SwissParam for CHARMM forcefield, how can i confirm that the > charges > > assigned are exact..?? > > > > You can see if they are correct in the sense of being a valid model of > reality by running a simulation and observing whether you can get > reasonable agreement with suitable e.g. experimental data. > > Mark > > > > Any help/suggestion is most welcome. > > Thank you... > > -- > > With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > < > > https://mailtrack.io/install?source=signature&lang=en& > referral=cy16f01.di...@nitk.edu.in&idSignature=22 > > > > > -- > > 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. > -- With Best Regards, DILIP.H.N Ph.D Student -- 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.