Re: [gmx-users] topology file for n-propanol
On Wed, Nov 20, 2013 at 4:53 PM, Ehsan Sadeghi wrote: > Thanks Justin. Could you explain more? You meant that I don't need > topology file for propanol? How about g_b, g_a, g_d values? > > You need a topology, but what I'm saying is that it is very easy to do. CH3 and CH2 groups are uncharged except the CH2-O-H group, which you can take from serine. Look through common functional groups across molecules - they have the same parameters. That is the design of GROMOS and many other force fields. The bonded parameters can also be taken from similar groups. The g_* notation corresponds to the labeling defined in ffbonded.itp - b for bonds, a for angles, d for dihedrals. The functional groups to which they apply are described in ffbonded.itp. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] topology file for n-propanol
Thanks Justin. Could you explain more? You meant that I don't need topology file for propanol? How about g_b, g_a, g_d values? Best regards, Ehsan - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 20, 2013 1:14:23 PM Subject: Re: [gmx-users] topology file for n-propanol On Wed, Nov 20, 2013 at 3:30 PM, Ehsan Sadeghi wrote: > Hi gmx uses, > > I need the n-propanol topolgy file including coordinates,g_b, g_a, g_i and > g_d required in aminoacid.rtp file. I am using gromos force field. Does any > body have this file? > > In the GROMOS force fields, molecules are constructed from building block moieties. Alkanes and alcohols are trivial to put together using all existing parameters, because all you are dealing with are uncharged CH3 and CH2 UA types and a CH2-O-H at the end. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] topology file for n-propanol
On Wed, Nov 20, 2013 at 3:30 PM, Ehsan Sadeghi wrote: > Hi gmx uses, > > I need the n-propanol topolgy file including coordinates,g_b, g_a, g_i and > g_d required in aminoacid.rtp file. I am using gromos force field. Does any > body have this file? > > In the GROMOS force fields, molecules are constructed from building block moieties. Alkanes and alcohols are trivial to put together using all existing parameters, because all you are dealing with are uncharged CH3 and CH2 UA types and a CH2-O-H at the end. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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.
