Hi all users, When I use the editconf command to transform pdb file to gro file, it shows like this
Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/atommass.dat Opening library file /usr/share/gromacs/top/vdwradii.dat Opening library file /usr/share/gromacs/top/dgsolv.dat #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7 Warning: Number of atoms in atom.pdb is 0 WARNING: all CONECT records are ignored Read 0 atoms Volume: 0 nm^3, corresponds to roughly 0 electrons No velocities found And this is my original pdb file ATOM 1 Ab DNA 0.575 0.516 0.051 1.0 0.0 ATOM 2 Tb DNA 0.159 2.344 0.191 1.0 0.0 ATOM 3 S1 DNA 2.365 6.568 1.280 1.0 0.0 ATOM 4 S2 DNA 2.365 -6.568 -1.280 1.0 0.0 ATOM 5 P1 DNA -0.628 8.896 2.186 1.0 0.0 ATOM 6 P2 DNA -0.628 -8.896 -2.186 1.0 0.0 ATOM 7 S3 DNA -1.947 6.704 -4.660 1.0 0.0 ATOM 8 S4 DNA -1.947 -6.704 4.660 1.0 0.0 CONECT 1 3 CONECT 2 4 CONECT 3 1 5 CONECT 4 2 6 CONECT 5 3 7 CONECT 6 4 8 CONECT 7 5 CONECT 8 6 MASTER 0 0 0 0 0 0 0 0 8 0 8 0 END not very complex, only 8 atoms . And I find these atoms are not included in the gromacs so i defined them in the .atp file this Ab 134.1; Adenine base of DNA Tb 125.1; Thymine base of DNA S 83.11; Sugar of DNA P 94.97; Phosphate of DNA Can anyone of you help me sovle this problem? Thank you in advance Yang He _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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