Hi Justin, Thank you for your reply. I have followed the regular forms about pdb file but it still shows that :
___> 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 > So I think it is because that the atom types such as Sugar ,Adenine base are not recognized by the gromacs .Also, what I want to solve is that how to define these big atoms . Do you know how to define these big atoms in order to make the gromacs recognize them and creat the correct gro.file Thank you . Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Wednesday, October 15, 2008 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] transfer pdb to gro He, Yang wrote: > 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 > > The .atp file means nothing for editconf. > Can anyone of you help me sovle this problem? > It looks like the formatting of your .pdb file is irregular. A fixed format is required for proper detection of atoms and coordinates. See here: http://www.wwpdb.org/docs.html -Justin > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant 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-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 _______________________________________________ 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