Hi, I found that when the output format from editconf (gmx4) is PDB, atom name like H5'1 will be changed to 1H5'. For other four-character atom name like ABCD, editconf works properly.
example: editconf -f a.pdb -o b.pdb ============= a.pdb ================== ATOM 1 P DT 1 -1.848 4.613 1.141 1.00 0.00 ATOM 2 O1P DT 1 -2.880 4.343 2.135 1.00 0.00 ATOM 3 O2P DT 1 -0.455 4.129 1.433 1.00 0.00 ATOM 4 O5' DT 1 -2.282 4.044 -0.246 1.00 0.00 ATOM 5 C5' DT 1 -3.668 4.059 -0.487 1.00 0.00 ATOM 6 H5'1 DT 1 -3.929 4.396 -1.500 1.00 0.00 ATOM 7 H5'2 DT 1 -4.303 4.601 0.280 1.00 0.00 ============= b.pdb ================== ATOM 1 P DT 1 1.100 4.615 1.808 1.00 0.00 ATOM 2 O1P DT 1 2.094 4.346 2.840 1.00 0.00 ATOM 3 O2P DT 1 1.393 4.130 0.416 1.00 0.00 ATOM 4 O5' DT 1 -0.287 4.047 2.242 1.00 0.00 ATOM 5 C5' DT 1 -0.528 4.063 3.628 1.00 0.00 ATOM 6 1H5' DT 1 -1.541 4.400 3.889 1.00 0.00 ATOM 7 2H5' DT 1 0.239 4.606 4.263 1.00 0.00 editconf in gmx3 works fine in the above situation. Regards, Jian _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
