Dear All,<br><br>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:<br>
<br clear="all">[ IMD ]<br> [ atoms ]<br> NA opls_557 -.257 1<br> CR opls_558 .275 1<br> NB opls_559 -.563 1<br> CV opls_560 .185 1<br> CW opls_561 -.286 1<br> H opls_562 .306 1<br>
HA1 opls_563 .078 1<br>HA2 opls_564 .075 1<br>HA3 opls_565 .187 1<br>CT1 opls_139 .000 1<br>CT2 opls_139 .000 1<br>CT3 opls_139 .000 1<br>CT4 opls_139 .000 1<br>
HC1 opls_140 .060 1<br>HC2 opls_140 .060 1<br>HC3 opls_140 .060 1<br>HC4 opls_140 .060 1<br>HC5 opls_140 .060 1<br>HC6 opls_140 .060 1<br>HC7 opls_140 .060 1<br>
HC8 opls_140 .060 1<br>HC9 opls_140 .060 1<br><br> [ bonds ]<br>CT1 HC1<br>CT1 HC2<br>CT1 HC3<br>CT1 CT2<br>CT2 HC4<br>CT2 HC5<br>CT2 CT3<br>CT3 HC6<br>CT3 HC7<br>CT3 CT4<br>CT4 HC8<br>
CT4 HC9<br>CT4 CR<br> CR NB<br> NB CV<br> CV HA2<br> CV CW<br> CW HA3<br> CW NA<br> NA H<br> NA CR<br><br>And this is my pdb file (at least a portion of it):<br><br>ATOM 1 CT1 IMD 1 -4.438 3.334 2.988<br>
ATOM 2 CT1 IMD 2 0.588 3.313 0.517<br>ATOM 3 CT1 IMD 3 5.476 3.310 -2.216<br>ATOM 4 HC1 IMD 1 -4.134 2.590 3.731<br>ATOM 5 HC2 IMD 1 -5.525 3.438 3.047<br>
ATOM 6 HC3 IMD 1 -3.996 4.291 3.276<br>ATOM 7 HC1 IMD 2 1.480 3.111 1.117<br>ATOM 8 HC2 IMD 2 -0.266 3.349 1.200<br>ATOM 9 HC3 IMD 2 0.702 4.307 0.076<br>
ATOM 10 HC1 IMD 3 6.375 3.525 -1.633<br>ATOM 11 HC2 IMD 3 4.648 3.862 -1.761<br>ATOM 12 HC3 IMD 3 5.628 3.709 -3.223<br>ATOM 13 CT2 IMD 1 -3.996 2.922 1.581<br>
ATOM 14 HC4 IMD 1 -2.902 2.862 1.545<br>ATOM 15 HC5 IMD 1 -4.281 3.703 0.865<br>ATOM 16 CT2 IMD 2 0.394 2.242 -0.557<br>ATOM 17 HC4 IMD 2 -0.485 2.486 -1.167<br>
ATOM 18 HC5 IMD 2 1.250 2.252 -1.242<br>ATOM 19 CT2 IMD 3 5.188 1.805 -2.247<br>ATOM 20 HC4 IMD 3 6.018 1.286 -2.742<br>ATOM 21 HC5 IMD 3 4.300 1.615 -2.864<br>
ATOM 22 CT3 IMD 1 -4.587 1.582 1.127<br>ATOM 23 HC6 IMD 1 -5.682 1.638 1.161<br><br><br>However when I run the code "pdb2gmx -f filename.pdb" I get the following error:<br><br>
"Fatal error:<br>Residue 'MD' not found in residue topology database"<br><br>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.<br>
<br>Jacob Harvey<br><br>-- <br>--<br>Jacob Harvey<br><br>Graduate Student<br><br>University of Massachusetts Amherst<br><br><a href="mailto:j.harv8@gmail.com">j.harv8@gmail.com</a><br>