Hi everyone,<br><br>I made a hole in a dppc128 bilayer, after that I merged the bilayer of hole with the protein manully (just copy and paste), then I want to do a EM with the merge.pdb.<br>But when I did pdb2gmx, choosing the 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) force field, I got a error told me that: Residue 'DPP' not found in residue topology database. The output of pdb2gmx run is below:
<br><br>Reading merge.pdb...<br>Read 12520 atoms<br>Opening library file /home/dong/programs/gromacs_hole/share/top/xlateat.dat<br>13 out of 13 lines of xlateat.dat converted succesfully<br>Opening library file /home/dong/programs/gromacs_hole/share/top/aminoacids.dat
<br>Analyzing pdb file<br>There are 28 chains and 1 blocks of water and 4104 residues with 12520 atoms<br><br> chain #res #atoms<br> 1 'A' 1 50<br> 2 'B' 1 50<br> 3 'C' 1 50<br> 4 'D' 1 50
<br> 5 'E' 1 50<br> 6 'F' 1 50<br> 7 'G' 1 50<br> 8 'H' 1 50<br> 9 'I' 1 50<br> 10 'J' 1 50<br> 11 'K' 1 50<br> 12 'L' 1 50<br> 13 'M' 1 50<br>
14 'N' 1 50<br> 15 'O' 1 50<br> 16 'P' 1 50<br> 17 'Q' 1 50<br> 18 'R' 1 50<br> 19 'S' 1 50<br> 20 'T' 1 50<br> 21 'U' 1 50<br> 22 'V' 1 50
<br> 23 'W' 1 50<br> 24 'X' 1 50<br> 25 'Y' 1 50<br> 26 'Z' 1 50<br> 27 ' ' 102 5100<br> 28 ' ' 321 2465<br> 29 '-' 3655 3655 (only water)<br><br>All occupancies are one<br>
Opening library file /home/dong/programs/gromacs_hole/share/top/FF.dat<br><br>Select the Force Field:<br> 0: Gromacs Forcefield (see manual)<br> 1: Gromacs Forcefield with all hydrogens (proteins only)<br> 2: GROMOS96 43a1 Forcefield (official distribution)
<br> 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)<br> 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)<br> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>4<br>Using ffG43a2 force field
<br>Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.atp<br>Atomtype 47<br>Reading residue database... (ffG43a2)<br>Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.rtp<br>Using default value - not generating all possible dihedrals
<br>Using default value - excluding 3 bonded neighbors<br>Residue 95<br>Sorting it all out...<br>Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.hdb<br>Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2-
n.tdb<br>Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2-c.tdb<br>Processing chain 1 'A' (50 atoms, 1 residues)<br>Opening library file /home/dong/programs/gromacs_hole/share/top/specbond.dat<br>5 out of 5 lines of
specbond.dat converted succesfully<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br>Fatal error: Residue 'DPP' not found in residue topology database<br><br>Then, I switched to use the 0: Gromacs Forcefield (see manual), it seemed that it ran normally except a warning: 'DPP' not found in residue topology database, trying to use 'DPPC'. I neglected this warning and continued, but when I did the "grompp" step, it gave the following messages:
<br><br>creating statusfile for 1 node...<br>Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar<br>checking input for internal consistency...<br>calling /lib/cpp...<br>processing topology...<br>Generated 1125 of the 1326 non-bonded parameter combinations
<br>WARNING 2 [file "merge_A.itp", line 69]:<br> No default Bond types, using zeroes<br>WARNING 3 [file "merge_A.itp", line 70]:<br> No default Bond types, using zeroes<br>WARNING 4 [file "merge_A.itp", line 71]:
<br> No default Bond types, using zeroes<br>WARNING 5 [file "merge_A.itp", line 177]:<br> No default Angle types, using zeroes<br>WARNING 6 [file "merge_A.itp", line 178]:<br> No default Angle types, using zeroes
<br>WARNING 7 [file "merge_A.itp", line 179]:<br> No default Angle types, using zeroes<br>WARNING 8 [file "merge_A.itp", line 180]:<br> No default Angle types, using zeroes<br>WARNING 9 [file "merge_A.itp", line 181]:
<br> No default Angle types, using zeroes<br>WARNING 10 [file "merge_A.itp", line 182]:<br> No default Angle types, using zeroes<br>Cleaning up temporary file grompp8Crm9R<br>Fatal error: Too many warnings, /home/dong/programs/gromacs_hole/i686-pc-linux-gnu/bin/grompp terminated
<br><br>I think there's some problem in my *.top file, but I don't know how to do with it, could anybody give me some suggestion?<br>My dppc128.pdb file is from: <a href="http://moose.bio.ucalgary.ca/index.php?page=Downloads">
http://moose.bio.ucalgary.ca/index.php?page=Downloads</a><br>