Thanks for your help Justin. Looks like I am still having issues though. Now I get the error: <br><br>"Fatal error:<br>Residue 'IMD' not found in residue topology database"<br><br>I am trying to create a topolgy file using pdb2gmx with the OPLS-AA force field and I have added the following entry to the ffoplsaa.rtp file. Also I have added IMD to aminoacid.dat but I dont think that is necessary for running pdb2gmx. Any ideas where I'm going wrong?<br>
<br>Jacob<br><br>[ IMD ]<br><br> [ atoms ]<br> NA opls_557 -0.257 1<br> CR opls_558 0.275 1<br> NB opls_559 -0.563 1<br> CV opls_560 0.185 1<br> CW opls_561 -0.286 1<br>
H opls_562 0.306 1<br> HA1 opls_563 0.078 1<br> HA2 opls_564 0.075 1<br> HA3 opls_565 0.187 1<br> CT1 opls_139 0.000 1<br> CT2 opls_139 0.000 1<br>
CT3 opls_139 0.000 1<br> CT4 opls_139 0.000 1<br> HC1 opls_140 0.060 1<br> HC2 opls_140 0.060 1<br> HC3 opls_140 0.060 1<br> HC4 opls_140 0.060 1<br>
HC5 opls_140 0.060 1<br> HC6 opls_140 0.060 1<br> HC7 opls_140 0.060 1<br> HC8 opls_140 0.060 1<br> HC9 opls_140 0.060 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><div class="gmail_quote">On Sat, Apr 4, 2009 at 7:36 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Jacob Harvey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
[ 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>
</blockquote>
<br></div></div>
It looks like you're off by a space in the format of your .pdb file, so pdb2gmx is not seeing the initial "I"; I posted the link to the PDB format guide the other day; have another look and see where you may have gone wrong.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Jacob Harvey<br>
<br>
-- <br>
--<br>
Jacob Harvey<br>
<br>
Graduate Student<br>
<br>
University of Massachusetts Amherst<br>
<br>
</div><a href="mailto:j.harv8@gmail.com" target="_blank">j.harv8@gmail.com</a> <mailto:<a href="mailto:j.harv8@gmail.com" target="_blank">j.harv8@gmail.com</a>><br>
<br>
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Virginia Tech<br>
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</blockquote></div><br><br clear="all"><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>