[gmx-users] Output of rotation
Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- 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] Output of rotation
Hi Shima, How did you rotate the structure? Probably the TER records got lost in the process. Cheers, Tsjerk On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Output of rotation
The input file has TER between 2 monomers. The command which I use is: #editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro After that, I use editconf to convert .gro to .pdb file: #editconf -f protein-rotate.gro -o protein.pdb The residue numbers after 10th one of output pdb file are changed and not correct. Sincerely, Shima - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, September 30, 2012 12:17 PM Subject: Re: [gmx-users] Output of rotation Hi Shima, How did you rotate the structure? Probably the TER records got lost in the process. Cheers, Tsjerk On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
