Section 5.3.3 of the manual. Catch ya,
Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 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: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Markus K. Dahlgren > Sent: Wednesday, 7 December 2011 4:47 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] dihedral format in top file? > > Hi, > > I am inexperienced with gromacs and I would like to figure out the > format of all > parts of a .top file, needed for Gromacs. I am trying to understand the > input > format so I can write a program for automatic setup for small molecule > ligands > with Gromacs, using the oplsaa force field. I have recently written a > C++ > program that converts BOSS autoput and creates NAMD input. Now I would > like to > do a similar program for Gromacs. > > I would like to write as few files as possible. I have some problems > understanding the format of the dihedrals in the .top file. I have > pasted the > top file for methanol I have been preparing manually below. Please > point out > any errors. Any pointers would be greatly appreciated. > > Methanol 4 > > [atoms] > 1 opls_157 1 UNK C00 1 -0.043617 > 2 opls_154 1 UNK O01 1 -0.586987 > 3 opls_156 1 UNK H02 1 0.074589 > 4 opls_156 1 UNK H03 1 0.074589 > 5 opls_156 1 UNK H04 1 0.074589 > 6 opls_155 1 UNK H05 1 0.406836 > > [bonds] > 1 2 1 0.14100 267776.00 > 2 6 1 0.09450 462750.40 > 1 2 1 0.14100 284512.00 > 1 2 1 0.14100 284512.00 > 1 2 1 0.14100 284512.00 > > [angles] > 4 1 2 1 109.50 292.880 > 5 1 2 1 109.50 292.880 > 6 2 1 1 108.50 460.240 > 3 1 2 1 109.50 292.880 > 4 1 5 1 107.80 276.144 > 5 1 3 1 107.80 276.144 > 5 1 4 1 107.80 276.144 > > [dihedrals] > 6 2 1 3 3 ?? > ... ?? > > > > If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how > do I > enter the information in the dihedral part of the .top file? The RB > parameters > for 6-2-1-3 is given below: > > C0 = 0.94140 > C1 = 2.82420 > C2 = 0.00000 > C3 = -3.76560 > C4 = 0.00000 > C5 = 0.00000 > > How do I enter this information into the .top file? > > Any help would be greatly appreciated! > > Thanks! > Best, > Markus > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
