R: Re: Re: [gmx-users] PTFE polymer chain
The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don't know if I made mistakes or simply I use badly the command. Thanks for the fast reply.Luana. Messaggio originale Da: jalem...@vt.edu Data: 09/04/2013 19.02 A: "luanadelore...@libero.it", "Discussion list for GROMACS users" Ogg: Re: Re: [gmx-users] PTFE polymer chain Please keep the discussion on the gmx-users list. On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it wrote: Hi Justin,thansk for the fast reply. The exact command is this:pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter I have created this directory coping the oplssa.ff directory in share utilities (I'm an user not an administrator of the pc) and I cannot modify the original files. I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and residuetypes.dat that I have modified addying the new residues. (I have also modifed specbond.dat for the two bonds between internal residue and starting/terminal residues. I don know if I made mistakes or simply I use bad the command. The command is incorrect. The -ff flag takes only the prefix of the force field you're trying to use. Your command is going to look for a directory called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put the custom oplsaa.ff directory in your working directory and issue pdb2gmx without the -ff flag. pdb2gmx will prompt you to choose the force field, allowing you to differentiate between oplsaa.ff in the working directory vs. the one in $GMXLIB. -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 listgmx-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
Re: Re: [gmx-users] PTFE polymer chain
Please keep the discussion on the gmx-users list. On Tue, Apr 9, 2013 at 12:55 PM, luanadelore...@libero.it < luanadelore...@libero.it> wrote: > Hi Justin, > > thansk for the fast reply. > > The exact command is this: > > pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter > > > I have created this directory coping the oplssa.ff directory in share > utilities (I'm an user not an administrator of the pc) and I cannot modify > the original files. > > I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and > residuetypes.dat that I have modified addying the new residues. (I have > also modifed specbond.dat for the two bonds between internal residue and > starting/terminal residues. > > I don know if I made mistakes or simply I use bad the command. > > The command is incorrect. The -ff flag takes only the prefix of the force field you're trying to use. Your command is going to look for a directory called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put the custom oplsaa.ff directory in your working directory and issue pdb2gmx without the -ff flag. pdb2gmx will prompt you to choose the force field, allowing you to differentiate between oplsaa.ff in the working directory vs. the one in $GMXLIB. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] PTFE polymer chain
On Tue, Apr 9, 2013 at 12:21 PM, luanadelore...@libero.it < luanadelore...@libero.it> wrote: > > Hi > I'm a new user of Gromacs and I want to construct a linear chain of > polytetrafluoroethylene using the force field oplsaa. > I created a work directory and I modified the rtp files by introducing 3 > new residues corresponding to my starter of chain (TFEa), my internal > residue (TFEi), and my terminal residue (TFEb)(following the same procedure > descirbed by Justin for Polyethylene) I add these new three residue to the > residuetypes.dat as Other. > When I run pdb2gmx with the -ff option (for using my modified force field) > the message of error is the following: > Could not find force field '/home/user01/work/oplsaa.ff/' in current > directory, install tree or GMXDATA path. > If I use pdb2gmx without using the command -ff the error is always the > same: > Fatal error: > Residue 'TFEa' not found in residue topology database > How can I solve this problem? Could someone help me? > It would be helpful to see your exact command, because my suspicion is you're invoking pdb2gmx incorrectly (it looks like you're specifying a path, rather than just a base force field name). The modified .ff directory needs to be either in $GMXLIB or in the working directory. If you omit -ff altogether, pdb2gmx will detect it automatically and allow you to interactively choose it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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] PTFE polymer chain
Hi I'm a new user of Gromacs and I want to construct a linear chain of polytetrafluoroethylene using the force field oplsaa. I created a work directory and I modified the rtp files by introducing 3 new residues corresponding to my starter of chain (TFEa), my internal residue (TFEi), and my terminal residue (TFEb)(following the same procedure descirbed by Justin for Polyethylene) I add these new three residue to the residuetypes.dat as Other. When I run pdb2gmx with the -ff option (for using my modified force field) the message of error is the following: Could not find force field '/home/user01/work/oplsaa.ff/' in current directory, install tree or GMXDATA path. If I use pdb2gmx without using the command -ff the error is always the same: Fatal error: Residue 'TFEa' not found in residue topology database How can I solve this problem? Could someone help me? Thanks! Luana. -- gmx-users mailing listgmx-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
