Thanks dear Erik.
Sincerely, Shima ----- Original Message ----- From: Erik Marklund <er...@xray.bmc.uu.se> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, September 17, 2012 2:05 PM Subject: Re: [gmx-users] Rotated protein Hi, Your pdb input (protein.pdb) is misformatted. Note that a pdb file is fix-format and that your residue sequence number is misaligned. As a consequence the last digit is not read for two digit residues. Erik 15 sep 2012 kl. 07.56 skrev Shima Arasteh: > Sorry for unclear explanation. > > 1. First step: > editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro > 2. Second step: > editconf -f protein-rotate.gro -o protein-rotate.pdb > > Some lines of protein.pdb are : > ATOM 59 CB PHE 9 -7.899 7.143 -7.348 1.00 0.00 > > ATOM 60 CG PHE 9 -8.253 5.762 -7.846 1.00 0.00 > > ATOM 61 CD1 PHE 9 -8.061 5.433 -9.193 1.00 0.00 > > ATOM 62 CD2 PHE 9 -8.775 4.811 -6.960 1.00 0.00 > > ATOM 63 CE1 PHE 9 -8.389 4.152 -9.654 1.00 0.00 > > ATOM 64 CE2 PHE 9 -9.103 3.530 -7.422 1.00 0.00 > > ATOM 65 CZ PHE 9 -8.910 3.201 -8.768 1.00 0.00 > > ATOM 66 N SER 10 -8.048 5.490 -4.333 1.00 0.00 > > ATOM 67 CA SER 10 -7.399 4.461 -3.545 1.00 0.00 > > ATOM 68 C SER 10 -7.862 3.074 -3.967 1.00 0.00 > > ATOM 69 O SER 10 -9.048 2.763 -3.893 1.00 0.00 > > ATOM 70 CB SER 10 -7.715 4.626 -2.061 1.00 0.00 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- 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
