Dear All, I am having issues editing a .rtp file (ffoplsaa.rtp to be exact). I want to create a new residue for my system so that I can generate a topology file using pdb2gmx. This is the code that I have added to the .rtp file:
[ IMD ] [ atoms ] NA opls_557 -.257 1 CR opls_558 .275 1 NB opls_559 -.563 1 CV opls_560 .185 1 CW opls_561 -.286 1 H opls_562 .306 1 HA1 opls_563 .078 1 HA2 opls_564 .075 1 HA3 opls_565 .187 1 CT1 opls_139 .000 1 CT2 opls_139 .000 1 CT3 opls_139 .000 1 CT4 opls_139 .000 1 HC1 opls_140 .060 1 HC2 opls_140 .060 1 HC3 opls_140 .060 1 HC4 opls_140 .060 1 HC5 opls_140 .060 1 HC6 opls_140 .060 1 HC7 opls_140 .060 1 HC8 opls_140 .060 1 HC9 opls_140 .060 1 [ bonds ] CT1 HC1 CT1 HC2 CT1 HC3 CT1 CT2 CT2 HC4 CT2 HC5 CT2 CT3 CT3 HC6 CT3 HC7 CT3 CT4 CT4 HC8 CT4 HC9 CT4 CR CR NB NB CV CV HA2 CV CW CW HA3 CW NA NA H NA CR And this is my pdb file (at least a portion of it): ATOM 1 CT1 IMD 1 -4.438 3.334 2.988 ATOM 2 CT1 IMD 2 0.588 3.313 0.517 ATOM 3 CT1 IMD 3 5.476 3.310 -2.216 ATOM 4 HC1 IMD 1 -4.134 2.590 3.731 ATOM 5 HC2 IMD 1 -5.525 3.438 3.047 ATOM 6 HC3 IMD 1 -3.996 4.291 3.276 ATOM 7 HC1 IMD 2 1.480 3.111 1.117 ATOM 8 HC2 IMD 2 -0.266 3.349 1.200 ATOM 9 HC3 IMD 2 0.702 4.307 0.076 ATOM 10 HC1 IMD 3 6.375 3.525 -1.633 ATOM 11 HC2 IMD 3 4.648 3.862 -1.761 ATOM 12 HC3 IMD 3 5.628 3.709 -3.223 ATOM 13 CT2 IMD 1 -3.996 2.922 1.581 ATOM 14 HC4 IMD 1 -2.902 2.862 1.545 ATOM 15 HC5 IMD 1 -4.281 3.703 0.865 ATOM 16 CT2 IMD 2 0.394 2.242 -0.557 ATOM 17 HC4 IMD 2 -0.485 2.486 -1.167 ATOM 18 HC5 IMD 2 1.250 2.252 -1.242 ATOM 19 CT2 IMD 3 5.188 1.805 -2.247 ATOM 20 HC4 IMD 3 6.018 1.286 -2.742 ATOM 21 HC5 IMD 3 4.300 1.615 -2.864 ATOM 22 CT3 IMD 1 -4.587 1.582 1.127 ATOM 23 HC6 IMD 1 -5.682 1.638 1.161 However when I run the code "pdb2gmx -f filename.pdb" I get the following error: "Fatal error: Residue 'MD' not found in residue topology database" Whats wrong with the way I edited the .rtp file? And why is pdb2gmx only recognizing the first two letter of the residue (why wouldn't it say "Residue IMD" because thats what I named it in the PDB file)? Thanks in advance for the help. Jacob Harvey -- -- Jacob Harvey Graduate Student University of Massachusetts Amherst [email protected]
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