Hi I don't have a .tpr file for the cg system. I am anlayzing results from pca and the trajectories only have calpha atoms. Can I generate a .tpr for just calpha?
> Date: Sun, 27 May 2012 12:12:14 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] trjconv -conect > > > > On 5/27/12 12:05 PM, vijaya subramanian wrote: > > > > Hi > > I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as > > follows: > > trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb > > > > or with one frame > > > > trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb > > > > but dont see any conect records in the output file. > > > > The conect records are in the input to -s , conect.pdb and in the following > > format: > > ... > > ATOM 4125 CA HIS X 173 107.816 143.564 71.946 1.00 0 > > ATOM 4126 CA THR X 174 110.288 142.372 69.327 1.00 0 > > ATOM 4127 CA LEU X 175 111.958 139.227 70.607 1.00 0 > > ATOM 4128 CA GLY X 176 108.771 138.107 72.357 1.00 0 > > CONECT 1 2 > > CONECT 2 3 > > CONECT 3 4 > > CONECT 4 5 > > CONECT 5 6 > > CONECT 6 7 > > CONECT 7 8 > > CONECT 8 9 > > CONECT 9 10 > > CONECT 10 11 > > CONECT 11 12 > > CONECT 12 13 > > CONECT 13 14 > > CONECT 14 15 > > CONECT 15 16 > > CONECT 16 17 > > CONECT 17 18 > > CONECT 18 19 > > CONECT 19 20 > > CONECT 20 21 > > CONECT 21 22 > > ... > > > > What should I do differently to get the conect records in the output file? > > > > > > Try using a .tpr file, where bonds are present according to the topology. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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
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