Dear gmx-users,<br>I am trying to run a simulation of a pdb with DNA molecule.<br>I have give gromacs force fied and the error i found was,<br><br>There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms<br><br> chain #res #atoms<br> 1 'A' 162 1245<br> 2 'B' 162 1245<br> 3 'C' 21 417<br> 4 'D' 21 428<br> 5 'E' 6 6<br><br>All occupancies are one<br>Opening library file /usr/local/gromacs/share/top/ffgmx.atp<br>Atomtype 52<br>Reading residue database... (ffgmx)<br>Opening library file ffgmx.rtp<br>Residue 50Fatal error: Atom type OWT4 (residue HO4) not found in atomtype database<br><br>Although there are posts to use the PRODRG, but it gives error that more than 300 atoms cannot be processed.<br>i am able to do simulation the pdb without
DNA.<br>but with protein-dna complex it shows the above error.<br>what may be the solution ?<br>Regards,<br>A.Raj<br><br><b><i>gmx-users-request@gromacs.org</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Welcome to the gmx-users@gromacs.org mailing list!<br><br>To post to this list, send your email to:<br><br> gmx-users@gromacs.org<br><br>General information about the mailing list is at:<br><br> http://www.gromacs.org/mailman/listinfo/gmx-users<br><br>If you ever want to unsubscribe or change your options (eg, switch to<br>or from digest mode, change your password, etc.), visit your<br>subscription page at:<br><br> http://www.gromacs.org/mailman/options/gmx-users/alaguraj_v%40yahoo.com<br><br><br>You can also make such adjustments via email by sending a message to:<br><br> gmx-users-request@gromacs.org<br><br>with the word `help' in the subject or body (don't include the<br>quotes), and
you will get back a message with instructions.<br><br>You must know your password to change your options (including changing<br>the password, itself) or to unsubscribe. It is:<br><br> vmsapk<br><br>Normally, Mailman will remind you of your gromacs.org mailing list<br>passwords once every month, although you can disable this if you<br>prefer. This reminder will also include instructions on how to<br>unsubscribe or change your account options. There is also a button on<br>your options page that will email your current password to you.<br></blockquote><br><BR><BR>ALAGURAJ VELUCHAMY<br>c/o Dr.S.KRISHNASWAMY,<br>CENTRE OF EXCELLENCE IN BIOINFORMATICS,<br>MADURAI KAMARAJ UNIVERSITY,<br>MADURAI, TN.<br>Ph:09486148690<p> 
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