Hi Mark, Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0.
Could you provide something about the specbonds.dat or give some explanations. Thanks in advance. 2010/10/9 Mark Abraham <mark.abra...@anu.edu.au> > > > ----- Original Message ----- > From: lammps lammps <lammp2fo...@gmail.com> > Date: Saturday, October 9, 2010 19:27 > Subject: [gmx-users] how to write a rtp file for amido amine > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Hi everybody, > > > > I want to use pdb2gmx command to create a .gro file and a .top file for > PAMAM whose repeat unit is amidoamine ( attached ). > > > > / > > ---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure) > > \ > > > > The atom N have two same branches with --CH2--. I write the rtp file for > it as follows: > > > > [ atoms ] > > C1 opls_245 -0.050 1 > > ......... > > [ bonds ] > > C1 -N7 > > ....... > > C6 N7 > > N7 +C1 > > N7 +C1 > > > > It seems not work, which gives a wrong top structure. The question is > how can I deal with the two branches of N. Any suggestion is appreciated. > > pdb2gmx is intended only for work with linear heteropolymers. Any more > complex things (e.g. disulfides, branched structures) have to be engineered > using the specbonds.dat mechanism. > > Mark > -- > 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 > -- wende
-- 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