Thanks for Mark and Justin's help. But I have new questions as follows:
CYS SG 1 HEME FE 2 0.25 CYS2 HEME 1.residue name A 2.atom name A 3.number of bonds that this atom can form (does the number include the bonds of atom with H atoms?) 4.residue name B 5.atom name B 6.number of bonds that this atom can form 7.the reference length for searching for candidate bonds, the margin is ±10%( It seems the unreasonable length can result in the unexpected bond. does it? ) 8.the new name for residue A ( Why new residue name?) 9.the new name for residue B Thanks again. 2010/10/9 Justin A. Lemkul <jalem...@vt.edu> > > > lammps lammps wrote: > >> 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. >> >> > http://www.gromacs.org/Documentation/File_Formats/specbond.dat > > -Justin > > Thanks in advance. >> >> >> >> 2010/10/9 Mark Abraham <mark.abra...@anu.edu.au <mailto: >> mark.abra...@anu.edu.au>> >> >> >> >> >> ----- Original Message ----- >> From: lammps lammps <lammp2fo...@gmail.com >> <mailto: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 >> <mailto: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 >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> wende >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
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