Hi, I stripped the following from a script of mine. The original script did some additional things before, involving first a conversion from PDB to CNS format and later to GMX format. I rearranged it without testing. You can try it and if you find that it doesn't do a proper job, you can send me the before and after file.
Hope it helps (hope it works ;)) Tsjerk ### #!/bin/bash # RENAME RESIDUES DNA_PDB2GMX='s/\(^.\{17\}\)DG /\1DGUA/; s/\(^.\{17\}\)DA /\1DADE/; s/\(^.\{17\}\)DC /\1DCYT/; s/\(^.\{17\}\)DT /\1DTHY/' RNA_PDB2GMX='s/\(^.\{17\}\) G /\1 GUA/; s/\(^.\{17\}\) A /\1 ADE/; s/\(^.\{17\}\) C /\1 CYT/; s/\(^.\{17\}\) U /\1 URA/' # RENAME ATOMS AND DELETHE HYDROGENS NUCL_DELHYD="/^.\{13\}H.'/d; /^.\{13\}H7..THY/d; /^.\{12\}H5''/d" THY_C72C5M='s/\(^.\{13\}C\)7 .THY/\15M.THY/' NUCL_PDBS2GMX="$NUCL_DELHYD; $THY_C72C5M; s/\(^.\{12\}...\)'/\1\*/" sed -e "{ $NUCL_PDB2GMX; $DNA_PDB2GMX; $RNA_PDB2GMX }" $1 On Sat, Oct 17, 2009 at 3:08 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > David Crosby wrote: >> >> Hello fellow GROMACS users! >> >> I've been having a heck of a time with the reformatting of a DNA molecule >> into a GROMACS-compatible format. I know that residues (bases) must be >> renamed to DTHR, etc., though it would be endlessly helpful if someone >> could >> please send me an example pdb or gmx file I can use as reference. Better >> yet, if anyone has a nifty program that will reformat a nucleic acid model >> into the GROMACS format, that would answer my prayers! The duplex I'm >> working with is only 21nt, so it's not insane to have to modify the file >> by >> hand... >> > > A simple Perl script can make substitutions, or you can use a text editor > like vi or a command like sed. In about 4 commands, the whole file can be > re-named. In vi, for example: > > :1,$s/DT /DTHY/g > > ...and all of your thymines are re-named (note the spacing is important). > > -Justin > >> Thanks in advance! >> Dave Crosby >> >> University of California, Irvine >> Dept of Pathology and Laboratory Medicine >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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/mailing_lists/users.php