<div>Hi,<BR><BR>My molecule is the cycloheptapeptide which contains a proline ring. The first problem is the disapperance of 7 hydrogen atoms in rtp file, so I run pdb2gmx with -ignh to ignore them and using Gromacs force field. The second one is the warning that atom <SPAN id=lw_1187093514_0 style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed; HEIGHT: 1em">CA</SPAN> not found in residue 8 while adding atom.<BR><BR>How does to solve with this?</div> <div>I try to pose the pdb in Prodrg site for a request of the .top file, but anything turns to me for 3 weeks.</div> <div><BR>It appears after select a forcefield like this:<BR><BR>Opening library file /usr/share/gromacs/top/ffgmx.rtp<BR>Opening library file /usr/share/gromacs/top/aminoacids.dat<BR>Reading TrialcordyhepA.pdb...<BR>', 64 atomshepA<BR>Opening library file /usr/share/gromacs/top/xlateat.dat<BR>26 out of 26 lines of xlateat.dat converted succesfully<BR>Analyzing pdb file<BR>There are 1 chains and 0
blocks of water and 22 residues with 64 atoms<BR><BR> chain #res #atoms<BR> 1 ' ' 22 64<BR><BR>All occupancies are one<BR>Opening library file /usr/share/gromacs/top/ffgmx.atp<BR>Atomtype 54<BR>Reading residue database... (ffgmx)<BR>Opening library file /usr/share/gromacs/top/ffgmx.rtp<BR>Residue 98<BR>Sorting it all out...<BR>Opening library file /usr/share/gromacs/top/ffgmx.hdb<BR>Opening library file /usr/share/gromacs/top/ffgmx-n.tdb<BR>Opening library file /usr/share/gromacs/top/ffgmx-c.tdb<BR>Processing chain 1 (64 atoms, 22 residues)<BR>There are 7 donors and 8 acceptors<BR>There are 12 hydrogen bonds<BR>Checking for duplicate atoms....<BR>Now there are 23 atoms. Deleted 41 duplicates.<BR>Opening library file /usr/share/gromacs/top/specbond.dat<BR>5 out of 5 lines of specbond.dat converted succesfully<BR>N-terminus: NH3+<BR>C-terminus: COO-<BR>WARNING: atom CA not found in residue 8 while adding
atom<BR>-------------------------------------------------------<BR>Program pdb2gmx, VERSION 3.3<BR>Source code file: genhydro.c, line: 304<BR><BR>Fatal error:<BR>Atom CA not found in residue Tyr8 while adding hydrogens<BR>-------------------------------------------------------<BR><BR>Thank you in advance,<BR>Nuch<BR><BR></div><p> 
<hr size=1>Boardwalk for $500? In 2007? Ha! <br><a href="http://us.rd.yahoo.com/evt=48223/*http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow">Play Monopoly Here and Now</a> (it's updated for today's economy) at Yahoo! Games.